The game consists of nine scenes, divided equally among three acts. I'll try to keep spoilers to a minimum, but some of them are impossible to avoid.
Act I
Scene 1: Origin
The opening scene of the game is a retelling of the death of Bruce Wayne's parents and otherwise non-interactive (you can look around, but that's about it). Enjoy the slightly freaky perspective as everyone else looks like giants since you are supposed to be in the body of a child.
Scene 2: Mansion
Wait for Alfred to come over and talk to you. He'll offer you a key, then tell you to meet him in the Batcave. Use the key to unlock the piano in front of you, open the cover to reveal the keys. While you could explore the rest of the room now, there is nothing else you need to do here, and you will need to search this room as part of the second pass of the game, so its up to you to if you want to take the time. The game has a number of interesting objects, background, and Easter Eggs (essentially) unrelated to achievements, so it is up to you when and whether you want to explore and examine them. When you're ready to proceed, press a few keys on the piano until you find the one that is out of tune, which will start the elevator and move you to the next scene, unlocking the first achievement:
Scene 3: Suit Up
Become the Bat! In this scene, you get to put on Batman's gear and learn how to use the basic tools you have at your disposal. Once the elevator stops and the Batsuit is presented to you, grab the bat symbol on the chest and bring it to you to put on the suit. At the next step, grab both handles with your hands to put on the gauntlets. Finally, grab the mask (cowl) and place it on your head.
You now get a view of yourself in a mirror. Enjoy moving your head and arms and watching Batman respond.
The next step relates to gadgets. You'll be presented with the Batclaw. Pick it up and point it at the test target in front of you, firing it by pulling the trigger. When you're done, you can drop it by putting your arm by your belt and pushing the grip buttons to release it. You can pick it up off your belt the same way (and look down to see it hanging there). All of your gadgets are stored on the belt.
The second gadget is the Scanner. Grab it, use it to scan the test object in front of you, then put it on your belt. Finally, the Batarang. Grab it, then throw it at the target in front of you. You don't really have to aim all that much, it will automatically curve toward the obvious target. Three more targets appear. You have an infinitely supply of Batarangs on your belt, so grab and throw to break all three targets. You can also flick them off of your belt with practice for faster throws, a trick that will become useful for some achievements down the road.
Once you're done with that, a big handle will appear. Pull it to descend to the Batcave and move on to Act II.
Act II
Scene 1: Batcave
Start by progressing the story; we'll explore the cave shortly. Wait for Alfred to come over and interact with him to find out what you need to do. Use the Batclaw to head over to the Batcomputer. Pull the lever to start it up. You'll see a computer panel on the side, where you can choose a character to learn more about them. Choosing a character will cause a life-sized hologram to appear in front of you, which you can rotate using the bar in front of them to see them from all sides. On the left are some cartridges. Putting one of these into the slot will cause the character to take a new pose or perform a basic action. To start, only three characters are available: yourself, Nightwing, and Robin. Load up Nightwing's profile and hit the tracking button to discover a clue as to where he is.
While you're here, right below the control panel is a tablet. When you pick it up, whichever hologram you're looking at will appear on it in smaller form, unlocking the achievement:
Head back to the forensics area where Alfred will suggest you take a vehicle to go find out what happened to Nightwing. Before doing that, look at the forensic station in front of you. There are a number of things you can do now or later, but let's take care of the achievement-related ones right now. There is a blood sample on the desk in front of you, along with a syringe and an empty tube. Three more blood samples are in a drawer on the right. Pick up the syringe and use it on yourself, then stick it in the empty tube to fill the tube. You now want to analyze all five samples. To do so, first put them in the centrifuge on the right and hit the button to spin them (you can do up to three at a time). Next, turn back to the left and grab the handle to raise a cylinder. Put a blood sample in the cylinder, lower the cylinder to start analysis. Repeat this for all five samples to unlock
Also on the left side of the forensics station you'll see three switches. Flip all three to start a Batarang challenge. You'll get a series of random targets in two colors. You need to hit all of the non-red targets as fast as possible. Every time you clear a level you gain a few more seconds. Hitting a red target will cost you a point. If you're aiming toward a section without red targets, definitely flick from the waist to save time; if you are aiming toward both a good and bad target, you might want to throw more deliberately, and try to aim outside the good target on the opposite side from the red one. As long as you're close to the right direction the Batarang will automatically curve into what you were aiming for. Your goal is to get a score of 30 or better, which is not very hard with just a little practice. Scoring 30+ will unlock:
One last achievement to get right now. Head to the Case Files section to the right and behind the forensics area. You can use this to examine a little bit of info about the first two Batman: Arkham games, as well as a section on the Riddler. Choose the Riddler, then choose one of his artifacts. This will cause a broken version of the artifact to appear on the holographic projector. Grab the various pieces and manipulate them to put them back together (you can see what the object is supposed to look like in the computer display). This can be a little annoying because they won't necessarily stay where you put them and will drift around a bit, although once two pieces are attached they stay that attached. Repeat for all three Riddler artifacts to unlock:
You can continue to explore if you wish, but when you're ready to move on, head over to the Garage area. Press a button on the panel to bring up one of the vehicles (you start with access to two). Before leaving, use the levers to maneuver the vehicle so you're looking at its back and press up on the circle pad to activate the vehicle thrusters and unlock:
When you're ready, pull the lever to move onto the next scene.
Scene 2: Dead End
You start on an upper fire escape. Before doing anything else, turn around and look in the window. You'll see some Mad Hatter paraphernalia. To unlock an achievement, you have to zoom in on it, which you do by reaching up to your head and holding the grip buttons (this interface action is never explained anywhere). Doing so while looking in the window will unlock:
Head down to the bottom of the alley to the body. Use the scanner on the body and follow the instructions to analyze the scene. Once you get to the right point, you can advance or rewind the action by tiling the controller left or right; pulling the trigger will scan. You need to find the three places where he is injured. The first happens early on when he gets punched in the face; stop the scene and press the trigger. The next is the breaking of the arm. Let the fight advance for a while and it's fairly obvious where it occurs. The final one is when the victim tries to escape up the building and gets knocked back down; as he falls he bounces off of the fire escape: this is when he breaks his ribs. Finally, play the scene forward until his neck is snapped.
You've now discovered there is a witness. Move down the alley so you can see where the witness was hiding and play the scene back and forth until you see him put his left hand on the wall near his head. Scan at that point to check his fingerprints and discover who he was. When the Batplane comes by, use the Batclaw to go to it and advance to the next scene. You should also unlock another story achievement about now:
Scene 3: Tipping Point
You find the Penguin punishing some of his henchman. You can listen as long as you want, but when you're ready, use a Batarang on the fire extinguisher to cause a distraction. You'll automatically dispose of the goons and string the Penguin up. He'll talk for a while, then some new goons will show up behind you. You can't attack them directly, instead (once Alfred gives you the go-ahead) focus your gaze on each one for a few seconds until a target-lock appears. Once all three are marked the Batplane will take them out. Once it's all done, you can grapple back to the plane and move on to the final act.
Act III
Scene 1: Shrapnel
You start in the morgue by a body. Look at the clipboards for more information. Eventually you're told to scan the body. Do so to find a piece of shrapnel, holding the trigger to identify it. Double pull the trigger to change scanning mode and repeat to find another piece of shrapnel. You are now able to move about the room. Head to the second corpse to the right. Scan twice (once in each mode) and find two more pieces of shrapnel. Finally, head over to where the cadaver drawers are. The door is locked. The nearby clipboard tells you the key is in the safe. Head to the safe in the corner (to the right of the cadaver drawer) and use the scanner on it. Three buttons are smudged. You can guess the combination by trying all six three digit combos of those three numbers or just type 425. Open the safe, grab the key, then head back to the drawer and use the key to unlock it. Once unlocked, pull out the cadaver and scan once in each mode again to find the last remaining shrapnel. You are now presented with a 3D puzzles to put the pieces of the bomb back together. Rearrange them and reveal a serial number, which will lead you to the next location.
Before leaving, however, we can unlock two more achievements. Look in the body drawer of the third body to find a keycard on the rail on the left side. Head to the corner of the room between the third body and the first body (opposite side from the safe). There is a tape recorder here, where you can hit play a few times to hear the coroner's thoughts. Use the keycard to unlock the nearby security cabinet and reveal items from previous cases. Scan all four to unlock:
Grab the anatomical model piece (a lung) nearby and head back to the safe. Place the lung on the model next to the safe, then grab the other pieces lying around and add them back onto the model, to unlock
That is it for now. Use the Batclaw to head to the plane and the next scene.
Scene 2: Bird Cage
Head into the sewer and down the corridor. When you come to a gate, use a Batarang to open the panel, then the Batclaw to pull the lever. Continue forward until you reach a place with Robin below. Use the Batclaw to swing down to him, then watch what unfolds.
Pull the cover off the panel to reveal a fuse box. One of the fuses is burnt out; remove it and throw it away. Eventually Robin will give you a third fuse. Rearrange them into the proper order (each fuse has a number on the bottom; the proper order can be found written in the box on Robin's side: A=10 top, B=20 middle, C=15 bottom). Once they are all in place and the panel charges, press the button to see the cage momentarily become electrified. This also opens another box on Robin's side with some gears.
Killer Croc will attack Robin. Hit the button again to shock him and make him leave. You now need to find more gears. They can be found in boxes scattered on the walls outside the cages. Use a combination of Batarangs and Batclaws to grab them, handing each one to Robin as you go. Killer Croc will attack you when you try to get the third one, so hit the button to shock him again.
Once the gears are in place, pull the lever to free Robin. He'll set about freeing you. You can't do anything more at this point beyond watching and eventually you'll find yourself in a descending elevator starting the next scene.
Scene 3: Reflectiosn
Once the elevator opens head forward to find yourself in Arkham Asylum. Go down the hall and press the button through the reception office opening to unlock the door on your right. Head to the end of the room and press the button; it shorts out rather than opening the door. You can see another button on the other side; use the Batarang to open it. Head in to find three prison doors. Each door has a window you can lower to look in. The first one you open (I don't think it matters which of the three you choose, it's always the first one you open) will hold Scarface (the Ventriloquist dummy). The second will hold Zsasz. The third will reveal Joker. He'll talk to you and ask you to lean closer. Once you do this you'll find yourself in a new location with a series of written clues on the walls and an ongoing conversation with Joker. You need to keep looking around and changing the direction your face to advance to the next part, but there's nothing else you really need to specifically do. If the game seems to have stopped advancing, look around until you find something that wasn't there before (e.g., a mirror may appear or disappear). Eventually all is revealed and the final story achievement will unlock:
After the credits, you end up back on the main menu, but something has changed...
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