Note: As stated in the Walkthrough Overview, there are achievements for doing absolutely every mission and activity in co-op. If you would not like to play the game twice, start the game up with a friend if you can.
When you start a new game, you'll be given three difficulty options. None of these pertain to specific achievements, so if you want to just breeze through things you're free to play on Casual. If you regret your choice, you can always change the difficulty in the pause menu's options. The way quests are handled is that some contain several parts, all of which should end in a quest complete screen. When reading the titles of these quests (the larger, centered text below), the format is [Primary Quest]: [Quest Segment].
Purple Ops: Zero Saints Thirty
After the events of Saints Row: The Third, the Saints have gained so much power that they're being sent on a mission to assassinate a target. Kinzie Kensington places her faith in Asha Odekar, one of her contacts to help you with the mission. The Boss's mic is coincidentally not working so you can't hear their voice, and they're covered entirely in their gear for the time being. Upon entering the terrorist base, the conversation between Kinzie and (surprisingly) Matt Miller reveal the person you're here to kill and how much is at stake. His motives are almost identical to those of a particular snake-y villain from another video game series.
Work with your fellow Saints to reach Cyrus and fight him with the prompts on screen when you see them, which will ultimately result in his nuke being launched. Run to the nuke as it launches and climb it - following more prompts when they appear - as the Saints say their last goodbyes to you. Upon disarming the nuke, you'll conveniently land right on the President's chair in the White House's oval office.
The success of this mission results in The Boss becoming so influential that he actually wins the presidency of the United States. Benjamin King from the long-dead Vice Kings gang serves as Chief of Staff. Your Vice President is the voice actor Keith David, known as The Arbiter, Sergeant Foley, David Anderson, and most importantly, Julius Little. You'll now be given the chance to develop what the President looks and sounds like; there are a lot of options in all categories to choose from, so you should easily find something you like.
Fun Fact: The "Silver Bullet" pose comes from an adult building of the same name in Chicago, where some of the developers were stationed at the time.
When developing a character, enter the Character Gallery menu and save your character. In some versions of the game, you need to have an account with saintsrow.com to make a connection to their databases and share the character, which will give you an achievement. In other versions, merely saving the character will give you the achievement, as the site has seen little use and is barely active (if active at all).
Hail to the Chief: The Saints Wing
As you walk to the conference hall, your Vice President will ask you to choose between two bills: You can either go down as the President who cured cancer, or the one who solved world hunger. Choose wisely. After this, an opposing politician will interrupt you; deal with him as you will, then move further toward the conference hall. After that, Josh Birk will invite you to watch Nyte Blade with Oleg. Accept or decline with your best interests in mind.
As Kinzie deals with reporters, aliens and their leader Zinyak will attack the White House. Fend them off and work your way out of the building so you can continue your defense against Zinyak's race. You'll actually find him in a battleship after you shoot it down.
Leave it to the Saints: A Pleasant Day
Just kidding - it was all a dream. Walk downstairs and get some breakfast, then go and get the newspaper. A police officer will offer to ride with you as you travel through Steelport; drive safely to the diner and wave as the people greet their President.
When things go awry, Kinzie will communicate with you and tell you to drive to the park. While you're there, wreak havoc as the game prescribes it. She'll send you a missile launcher so you can mess with "the simulation" faster; aiming for cars causes the most destruction here. When you inflict over $100,000 in damages, a supercop will pounce from above to take you down. The best way to accurately hit him with the missile launcher is to just aim for his feet, since that'll at least hit the ground underneath him. The cop's defeat will ultimately ruin the simulation you're placed in.
As a consequence, Zinyak will create a simulation of Steelport with a few changes: The Saints have no influence, the aliens have huge towers around the place, and there are ex-convict aliens sent after you just for the sake of torment.
Learn the Rules...: The Fundamentals
In the simulation, Kinzie will suggest you go buy a gun, since you're going to be here for a while. Hijack a car and use the hub menu to access the map and pinpoint Friendly Fire on your GPS. When you arrive, buy all three available weapon types before buying an upgrade. Buy any upgrade before you leave the store, then do what Kinzie says and defeat some Zin by a flashpoint (of which there are a total of 32). Kinzie will then tell you to head to her place so the two of you can use her gear, but it seems to have disappeared when Zinyak removed all Saint-ly influence.
For completing this quest, you'll finally get some real rewards in the form of Cache, XP, and a hack that delivers saved vehicles to your exact location. You now get to choose between the next main quest and a side quest. The latter teaches you more on character customization. When upgrading a vehicle (hijacking any will do), do not grow too attached to it. Vehicles are about to become completely obsolete. You'll mostly be selecting future quests through the hub menu.
Learn the Rules...: Time to Increase the Tempo
Continue the quest in the Quests tab of your hub menu. Kinzie will point out some data clusters near her warehouse that she wants you to collect for her. When you have enough, check the Powers tab in your hub menu and purchase the Super Sprint and Super Jump abilities for two data clusters each. Kinzie will set up a training program for you to test your abilities.
After the testing program, Kinzie will send you into your first Blazin activity, where you have to race to several checkpoints within a certain time. Collecting green orbs will boost your sprinting speed.
Learn the Rules...: Hot and Cold
Hotspots throughout the simulation are protected by generators, which are protected by Zin. The first one you come across will have just two generators, which you can disable as long as you aren't being shot at. Focus on killing the Zin that can shoot at you from a certain angle so you can disable the generators, then get to the main console and disable the hotspot entirely. This will prompt a warden to appear; fight him with your current supply of weapons (the shotgun should stun him out of certain attacks) until you deplete all of his health. After he's downed, run into him and absorb his Blast power.
In another training program, use your new Blast power (the first type you get freezes things) on some decoy Zin. Data clusters can also be hidden in walls, which require a blast to remove. Finally, wardens now have a shield that can be deactivated with a blast. Fire one at the sim Zin and then shoot it with a weapon.
The Escape: The Real World
Kinzie will figure out how to make your mind return to your body by having you walk through a certain door in the simulation. When you awaken, work your way through the Zin facility and defend your position until Kinzie and Keith David arrive to pick you up. Take command of the ship and try to contact Oleg before the line is cut short. Inspired more than ever to save the rest of the Saints and defeat Zinyak, the President will return back into the simulation through the new ship to take the fight to the Zin.
You'll now be able to leave the simulation to walk around the ship at any time. DLC content should activate after this quest as well, and you should have almost full capacity in completing tasks around the simulation. Now would be a good time to consult the other walkthrough pages on challenges, upgrades, and miscellaneous achievements so you can set some goals for yourself as you take control of pseudo-Steelport.
Note: You should now be getting some small side quests to complete specific activities in the world. These should be given to you by your fellow Saints, and most often lead to a final loyalty quest. Completing these before finishing the final quest is required for an achievement and doing things in general will make the game easier in the long run, so now would be a good time to get started on things.
Breaking the Law: Hack the Planet
To further gain control over the simulation, Kinzie suggests hacking stores to gain some benefits. Head to a Planet Zin nearby and start hacking it to enter a small mini-game. You'll need to connect the start and end of the board using the pieces shown on the right side of the screen within the time limit, shown at the top. This first one should be a simple line.
After taking over the store, police (and eventually Zin) will be alerted to your position, and you'll be introduced to portals that spawn enemies. These can be destroyed, and it's recommended that you do so right away. It's also worth noting that there's a destructible statue of Zinyak on the roof of the store. After enough destruction, a golden C.I.D. orb will spawn. Sprint after it and destroy it with the button/key prompt on-screen to remove your notoriety. After finishing this quest, chapters of Zinyak's life will be spread across the simulation. The game should also tell you about the Zinyak statues.
Breaking the Law: Break on Through
A strange voice will tell you that it will offer assistance in your goals, as long as you head to his "rift" and do what he says. This will be an introduction to the Platforming Rift activities, where you must properly aim your jumps to land on the center of dozens of platforms for more points. Having an upgraded Super Sprint and Super Jump would be beneficial, but are not required for this initial rift.
The A.I. will explain his situation to you: He's lost his body due to the Zin, and is willing to do anything for you if it means taking them down. All he needs is a physical body to take form in. More Platforming Rifts will appear throughout the simulation after this quest.
Breaking the Law: That Burning Sensation
The A.I. will offer you a new Blast power, giving it a fire essence. Simply test it out and you'll finish this quest.
You can complete all of Keith David's side quests by the end of this one. Unlike with other members of the Saints, you won't have to romance him as well in order to unlock his related achievement (you can't romance him at all). The last thing you'll get from Keith is the Roddy Piper outfit.
Ghost in the Machine: Power Up CID
In order to find a body for the A.I., you'll want to go to the ruins of the old Saints crib. Kinzie's plan is to capture a C.I.D. from the Zin and wipe it. Fortunately, there are a handful of C.I.D.s nearby, and along with it is a bounce rifle. These things shoot a pellet that bounce between enemies for serious damage. When you have a bounce rifle and a C.I.D. that works, take it to a nearby rooftop and protect it while Kinzie does all the tech work.
After Kinzie gets things set up, the process of downloading the A.I. into the core should take about 55 minutes. That's too long. Take the C.I.D. to the power plant for a more stable connection, then hold the Zin off until Kinzie locates a few more access points to speed things up even further. Having three access points at once will be too fast at first; cool the C.I.D. off with a Freeze Blast, then defend yourself for only a few more minutes as the A.I. enters the C.I.D. Now that the the two have merged, the Saints will refer to him as C.I.D.
A warden powered with Telekinesis will drop from above. Defeat him and absorb his power to use the ability, then test it out on the test rooftop.
Ghost in the Machine: Go to Training Program
To get the hang of your new TK powers, head to a new activity called Genki's Mind Over Murder (M.O.M.). Throw the marked items into the floating rings in the air to score points. Cars go in blue rings, people go in green ones, and the glowing pink Genki cat heads go in the pink ones. All of these will become available after finishing this first one.
You can complete all of C.I.D.'s side quests by the end of this one. Simply romance C.I.D. on the ship if you haven't already done so for an achievement.
Note: After this quest, the How the Saints Save Christmas DLC should now be available.
Zero Cool: Miller-Space
To rescue Matt, you'll need to return to the Broken Shillelagh and have C.I.D. connect your simulation to his. To reach it, Kinzie will set you up with a tank as you fight your way into the next simulation. A bike will appear for you to use after the tank has reached the end of the line. There won't be much in your way as you speed through Zinyak's digital army and end up somewhere else.
Zinyak will give you a choice between the red door or the blue door. Before you choose, look around at the boss's past being shown on monitors, then choose the red door for a missable achievement.
When the game reloads, choose the blue door to continue the game. You'll be treated to a text adventure with Metroid-esque music playing in the background. Below are instructions on how to finish the text adventure. It should be easy enough to figure out on your own, though.
*** Spoiler - click to reveal ***Approach the computer, tell it you're a slave, fly towards the purple star in the distance, and then enter it. Drink the wine in the next room and wake up on an island. On the island, make some cocktails and offer the architect a drink. A woman will appear after this. Tell her to let you go over and over again until she starts crying, then apologize profusely to make her feel better. Tell her that you wish to rescue Matt, and in response she'll tell you that you must fight Matt's most feared opponent.This opponent is Killbane, standing in a wrestling ring. Matt will appear on the other side of the ring, nervous and scrawny as per usual. Encourage him and make him punch Killbane a few times so he wins. Pick up the phone.
The Saints will realize that Matt probably needs some help getting to the ship. Well, Kinzie won't realize this. She just doesn't like him. Before starting the next quest, you'll be able to talk to Kinzie on the ship so the two of you can work on opening more gateways to spawn in from. These gateways are very handy, so keep helping her out as you play until all of them are done.
Zero Cool: Matt's Back
Head over to Kinzie with this quest active in the ship. She'll give you a very big suit of power armor that has properties of something you'd find on Mars. Try using your jets to fly upwards to a door your size and bash it open. You should be able to just blaze through the first set of rooms without having to worry about actually fighting the enemies. When you get to Matt, protect him as he finds parts for a weapon for the power armor and then head outside to meet up with Kinzie. Fight off several hordes of enemies and take Matt to the ship.
Man the turret on the back of the ship and help defend it until you all have made it to safety.
Anomalous Readings: The Warden Stomp
A warden will appear after entering the simulation, and this one specializes in stomping. Defeat the warden and absorb his power to earn a Stomp power of your own, then finish the training on the rooftop as with other powers.
Nytefall: Nytefall
This is the earliest opportunity to finish Matt's loyalty mission. Doing so will give him superpowers, making him more useful as a homie if summoned. You will want to upgrade some weapons if you haven't been doing so.
Matt wants to run a little simulation of his that he's very proud of. He won't tell you what it is until you get there. In this simulation, you can't use your powers. It won't take long for you to figure out that Matt has written some NyteBlade fan-fiction. It's a very simple plot; help NyteBlade fight off his enemies until Zinyak starts to edit his fan-fiction. On a terrible turn of events, the two of you must confront and defeat NyteBlade himself. After doing so, Matt will gain his powers for use within the simulation, and he'll also have earned the rights to all NyteBlade property.
After finishing this quest, simply romance Matt on the ship, if you haven't already done so, and finish all of his side tasks for an achievement.
Anomalous Readings: Super Power Fight Club
Now that you have three powers, the Super Power Fight Club activity will become available. Defeat three waves of enemies using only your powers to win the activity.
Back by Popular Demand: De Plane Boss
The boss is certain that Johnny Gat is alive and held within the plane prison due to the events of Saints Row: The Third. Fight through the Morningstar in the plane and reach the room he was killed in. It won't be Gat you'll find in there, but Shaundi. Zinyak will whisk her away and leave you in the plane. Jump across the light until you get to an old nightclub. Those of you who have played Saints Row 2 will enjoy this moment.
Veteran Child will have Shaundi held up as a human shield once more. Use the stun gun you suddenly have on you to tase him, then kill him when he's disabled. Zinyak will find this unfair and spawn in many Veteran Children (Veteran Childs). Trying to kill them will only make them multiply, but Kinzie will have a solution to this. A new weapon, the Disintegrator, will appear, and it'll permanently delete each Veteran Child in the room.
Note: After this point in the story, you'll be able to look for three more Saints in whichever order you choose.
Girls Night Out: Psychomatic
This is the earliest opportunity to finish Shaundi's loyalty mission. Doing so will give her superpowers, making her more useful as a homie if summoned.
Veteran Child has appeared in the simulation, and the two Shaundis will have the same idea: kill him. To make things easier, Fun Shaundi wants to get some alien drugs from a dealer before they attack Veteran Child. These drugs, when you do eventually find them, will give the Shaundis superpowers. Chase them as they race each other around Steelport and then defeat Veteran Child's waves of crowds. The man will then create more clones of himself, which get stronger the fewer there are. Defeat them all and finish Veteran Child off for good.
After finishing this quest, simply romance Shaundi on the ship, if you haven't already done so, and finish all of her side tasks for an achievement.
The Boss Goes to Washington: The Saints Flow
Pierce is locked away at the old Saints crib, being attacked by guys wearing Saints Flow costumes. Gather some weapons from within the crib and attack the biggest guy in costume. His name is Paul. Fire rockets at him and defend yourself from the regular-sized cans until Kinzie tells you to get to the island with a statue on it; Pierce will fly a helicopter to pick you up and take you there. Attack Paul to wake him up and lure him to the island, then get to the base the statue and use it to crush Paul to oblivion. Pierce will now be available as a homie, and he too will have things for you to do.
Pump Up the Volume: Brotherhood
This is the earliest opportunity to finish Pierce's loyalty mission. Doing so will give him superpowers, making him more useful as a homie if summoned.
Pierce will tell you his plan to draw out Zinyak's guys. The two of them will listen to the radio, and it's worth slowing down to listen to the song that plays. Destroy the trucks at the docks and sing along to the radio as you travel to the nuclear power plant. Collect some nuclear waste (what is this plan for?) and follow a Brotherhood truck to figure out where he's going. Don't bother following it with a car, just jump and fly around.
The guy Pierce is after is none other than Maero, leader of the Brotherhood. Kill this super-powered version of an old enemy and Pierce will get a really familiar costume to go with some new powers of his own.
After finishing this quest, simply romance Pierce on the ship, if you haven't already done so, and finish all of his side tasks for an achievement.
King of Stilwater: King Me
Benjamin King, leader of the Vice Kings, is stuck in Stilwater. A pocket of angry Vice Kings will be between you and the church on Third Street. However, more will arrive when you get close to the entrance. Find Ben in the church and help him defeat his former gang as he plots against Tanya and Tony, who started the coup against him. Fight dozens of Vice Kings and wait for the two leaders to come after Ben King, then kill them. Breaking the cycle of King's simulation will free him from his prison.
Emergency Situation: A Game of Clones
This quest will appear after rescuing two Saints, and you will constantly be attacked until it's been dealt with. Enter the simulation and look at how many enemies Zinyak is pouring inside of it. There are a few relays blocking the signal being transmitted by Zinyak. Chuck C.I.D. into the air so he can get a grasp of where the signal is, then destroy the relay that you find. This will happen a few times until Kinzie is able to find the portal the gangs are popping out of.
Upon reaching the portal, TK throw gang members back into it until a much more threatening foe comes out of it: yourself. This Saints Row 1 version of the boss has powers as well, and he's got a ton of health to boot. Wind him down and chuck him into the portal to defeat him, only to be treated to two co-op-player bosses from Saints Row 2. Do the same to them, and then face off against the warden that drops in to kill you. He'll grant you the Buff power, which you'll get to test on the rooftop like your other powers.
King of the Dance: Dancing Queen
This is the earliest opportunity to finish Benjamin King's loyalty mission. Doing so will give him superpowers, making him more useful as a homie if summoned.
After her escape, Tanya has been infecting people in the simulation with a virus that turns them into sex workers. You'll be tasked with absorbing this virus to weaken her forces, then head to Tanya's club. The boss won't be able to hold themselves in after entering the club. Tanya will have spotted you and left for the rooftop while you were busy. Catch up to her and fight her until you can chuck her over to the park so Ben can finish her off for good.
After finishing this quest, simply romance Ben on the ship, if you haven't already done so, and finish all of his side tasks for an achievement.
From Asha with Love: The Case of Mr. X
Asha's looking for someone as part of a mission. You're there as well, but you'll be looking very different. She's looking for your evil twin, who definitely isn't hiding out in a remote part of the world. Perform some tactical espionage action and take out the soldiers in your way very strategically, per Asha's instruction. You'll soon come across a man in a test tube, also wearing an eyepatch. Is this the evil version of you? We can't really make that out for now.
There are several guards in the room up ahead, and it's a good idea to sneak past them using a cardboard box. Kill the guards when sneaking up on them, and then move into the next room. You'll soon come across Mr. X speaking to you on a terminal, and afterwards he'll send about a dozen soldiers on your position. It won't be long until you find the bigger boss.
Kill Mr. X's henchmen and the man will step out himself to fire at you. After taking enough damage, he'll hide behind cover and you'll be prompted to shoot at some equipment. Quickly do this, because Mr. X will regain health if you allow him to sit behind cover uninterrupted. Keep doing this as more henchmen come to fight you and Asha until he's finally defeated.
Training Day: Asha's VIP
This is the earliest opportunity to finish Asha's loyalty mission. Doing so will give her superpowers, making her more useful as a homie if summoned.
Asha wants to unwind, but her definition of unwinding is a VIP escort mission. The first stop is a simple trip to a Planet Saints, nothing out of the ordinary. At the second stop, however, snipers will appear on the roof, and things will only get more hectic from there. Kill off all the agents trying to get the VIP and take her to the place where she's supposed to be picked up. An unruly Professor Genki will attack you when you arrive, killing the VIP instantly. After taking enough damage, the cat will transform into Super Genki, but he won't need any gemstones to do it. Matt will give you your powers back so you can stand a chance against Super Genki, and on top of that he'll give some to Asha as well. Kill the mad scientist to end this quest.
After finishing this quest, simply romance Asha on the ship, if you haven't already done so, and finish all of her side tasks for an achievement.
...the Very Next Day: Welcome Back
To reach Johnny, things are going to go a bit differently. He's being kept in so high a security that the simulations cannot connect so simply. Entering his simulation results in a game of Streets of Rage. This is a simple beat-em-up against the Vice Kings, who have surely deserved the reputation as being the most memorable gang from the first Saints Row at this point. This should be a simple enough game - just beat up the enemy and keep moving to the right. You'll be able to help Gat get over one of the most traumatic days of his life, releasing him from his pod in Zinyak's ship.
Take the power armor into the ship and try to locate Johnny, killing anyone that gets in your way. Johnny will have left a trail of Zin in his wake, making for an easy trail to follow. He'll explain what happened with him and the Morningstar after you get to him.
SR3 Wrap Up: Gat Time, Fun Time
This is the earliest opportunity to finish Johnny Gat's loyalty mission. Doing so will give him superpowers, making him more useful as a homie if summoned.
Johnny could use a run through Genkibowl. Take a trip there with him to get his spirits up. Fight through several rooms with Johnny and just have a good time catching up with him. Earn enough money to move to the next area. At the end of the Genkibowl, Matt has placed Philippe Loren so you can kill him one more time.
After finishing this quest, simply romance Johnny on the ship, if you haven't already done so, and finish all of his side tasks for an achievement.
Death From Above: Training
Death From Above is a new power learned after rescuing Johnny. Simply go through the motions of the training simulation with Kinzie so you know how to use it.
The Kinzie Gambit: When a Plan Comes Together
The Zin have ambushed Kinzie's hideout in Steelport, and this ambush includes grenades that temporarily remove your powers. Help everyone escape and take the chopper on the roof as you escort the other Saints on the ground. Use the choppers minigun and rockets to destroy all Zin that follow both their car and yourself.
The chopper will crash land on Professor Genki's building, of all places. Man the turret by one of the windows and go nuts killing the Zin that flood the killing floor. Be cautious of shooting the Sad Panda targets; those will shock you if you hit them. Hitting the Ethical targets will activate a trap to help you out. Defend the Saints' vehicle after they leave the building.
The Kinzie Gambit: All Hands on Deck
The Zin will have captured several Saints, as this entire thing was a setup. Defend the ship and find the bombs, then take them into the mothership and put them on the biggest, glowingest thing, as told by the game. Plant your bombs and return to the ship quickly so the remaining set of Saints can figure out a new plan.
The one responsible for this entire thing is the one that was totally the least expected.
Talkie Talkie
Talk to Matt Miller. That's just about it.
The Girl Who Hates the 50s: He Lives
Keith David will be working a rally within the simulation. Apparently, he bargained with Zinyak for power in exchange for his friends. Follow him into the federal building, where you'll see him have a change of heart at the last second. After being punished by Zinyak, you'll soon be greeted to a fistfight between Roddy Piper and Keith David. Keith will fly away in a panic; Roddy will explain that Keith thinks everyone is out to get him. Chase him to the roof and disable the satellite that's been brainwashing Keith. You'll be given a bunch of shots of Roddy performing a bunch of moves on Keith before he gets choked out right before telling you where Kinzie is.
This will free Keith of his brainwashing. Keith will comment that Roddy does not get called upon, but that he rather appears where he is needed most. This was one of those times.
The Girl Who Hates the 50s: Hello Teacup
Now to find Kinzie. C.I.D. will find a secret room that contains a confusing map of the simulation. You'll arrive in the 50's once again and you'll be looking for multiple Kinzie's until she manages to tell you where she is. None other than Cyrus Temple will be in charge of this simulation. Rewire the speakers in this town to disrupt his speech, destroying propaganda trucks along the way. The music should help free Kinzie a little bit, but it'll also tick Cyrus off. Fight him and Kinzie will be freed from this hell.
The Girl Who Beat Cyrus: Kinzie's Adventures
This is the earliest opportunity to finish Kinzie's loyalty mission. Doing so will give her superpowers, making her more useful as a homie if summoned.
The virtual Cyrus Temple has invaded the simulation and rebuilt his forces in his old base. Steal a tank and destroy all of the STAG equipment, then fight Temple until he's at a weak enough state for Kinzie to finally chime in and kill him for good.
After finishing this quest, simply romance Kinzie on the ship, if you haven't already done so, and finish all of her side tasks for an achievement.
Keymaster: We Have the Technology
Kinzie and Benjamin King have determined how to shut everything down. The Saints have to make a key, and the first piece is a CPU hidden inside the ex-STAG armory. Use TK to pry open containers until you find it. After you have that piece, you'll next have to destroy alien tech for six more pieces. The last thing you'll need are gravity inhibitors, found at the docks. Quickly make it over there before time expires and destroy more tech to get them. Help Johnny land the plane he took from the STAG armory and defend the area until Shaundi comes in to pick you up.
Keymaster: Batteries Not Included
The key now only needs a proper source of power. Meet C.I.D. on the east side of Steelport. There are three battery-like objects that C.I.D. is aware of. At each of these batteries, you'll need to locate the battery with the help of a proximity meter in the top left. Simply take the battery and leave to the next one until you have all three. All batteries are at ground level. Some of the batteries will be protected by shield generators. The third battery is encased within a tank, and it'll have to be driven back to Kinzie's warehouse. The power inside the battery is causing the tank to overload, meaning that if Kinzie doesn't shut it off within three minutes, it'll explode. Quickly drive it back to end the quest.
[message]Note: There's a missable achievement related to finishing the game that requires you to complete all of your friends' loyalty missions beforehand. Do not finish the game until you've completed all of these loyalty missions. This should get you very close to completing everything there is to do in the simulation, and you should aim to do so before starting the last set of quests.
These two achievements are given to you as you take over more and more of the simulation.
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Punch the Shark: Grand Finale (Part 1)
Return to the ship once all of your loyalty missions are complete. The boss will give a speech to his crew to motivate them before the final push on Zinyak. Pick any team to help with the first task.
The first thing that needs to be done is to take the key to the old Syndicate tower, causing the simulation to malfunction. Act as escort for the key as your first team drive it to the building. Use the weapons given to you to stop all of Zinyak's forces from destroying it. Use TK to bring the key to C.I.D. so he can do more technical work. Once inside the building, fight off the Zin and help C.I.D. so the key can reach its destination.
Punch the Shark: Grand Finale (Part 2)
Choose your next team and work with them to fight off more Zin as the simulation starts to collapse. Fight to defend one of three portals, then leave one of your teammates behind after gaining control of it. After the third portal, you'll have to get out of the simulation. Head to the gateways out of there until one of them decides to work; well, in one way or another. At the main menu of Saints Row, select Continue Game.
Punch the Shark: Grand Finale (Part 3)
This will automatically push you and your last team to Zinyak's ship once more. After pushing into the armory, you'll find some real power armor. This will give you the power given to you in the simulation. With the help of your power armor, you should be clear to dive down towards the throne room. Just get rid of a blast door after it closes and you'll be all clear to reach Zinyak.
Punch the Shark: Grand Finale (Part 4)
Zinyak, in his vanity, will broadcast this fight across the entire Zin Empire. Use the arm cannon on the power armor as well as your powers (Blast would be most effective) to weaken Zinyak's armor as his soldiers fight alongside him. After taking enough damage, he'll hide behind a shield surrounded by explosive C.I.D.s; use TK to throw them into the armor until these are ejected out of the arena. Kill enough of his Zin until C.I.D. unlocks the shield generators, allowing you to destroy them. Your fellow Saints should arrive during this process to aid in the fight.
When Zinyak has been ejected from his armor, perform several moves on him through quicktime events until Zinyak has finally been defeated. Your new servant, Zinjai, will inform you that the Zin, and now the Saints, are capable of time travel. A neat post-game scene will start, followed by the credits; both can be skipped, but you won't want to skip the first one.
And with that, the game is complete. If you've followed the previous advice on finishing the side content before reaching the end of the story, then you should only have to clean up on achievements you don't have, as well as the DLC content, if you own it.