Here is the full list of all 99 Time Clickers achievements. It takes around 200 hours to unlock all of the achievements on Windows.
Defeat Wave 3,000 Boss
Beat Wave 3,000
Get a Team Member to Spec Ops 5 (LVL 5,000)
Time Warp 250 Times
Collect 3.00M Weapon Cubes
Beat Wave 2,750
Collect 5.00M Time Cubes
Time Warp 100 Times
Beat Wave 2,450
Upgrade a Team Member 25.0K Times
Get a Team Member to Spec Ops 4 (LVL 4,000)
Beat Wave 2,150
Destroy 75.0M Cubes
Upgrade a Team Member 12.5K Times
Time Warp 50 Times
Defeat Wave 2,000 Boss
Destroy 1,000 Rainbow Balls
Destroy 50.0M Cubes
Beat Wave 1,850
Beat Wave 1,550
Get a Team Member to Spec Ops 3 (LVL 3,000)
Beat Wave 1,350
Upgrade a Team Member 5.00K Times
Beat Wave 1,150
Defeat Wave 1,000 Boss
Beat Wave 950
Beat Wave 750
Get a Team Member to Spec Ops 2 (LVL 2,000)
Collect 1.00t Gold (Total)
Time Warp 25 Times
Beat Wave 550
Destroy 1.50M Yellow Cubes
Collect 1.00r Gold (Total)
Shoot Click Pistol 250K Times
Defeat Wave 500 Boss
Collect 1.00p Gold (Total)
Upgrade a Team Member 2.00K Times
Collect 1.00n Gold (Total)
Beat Wave 350
Collect 1.00l Gold (Total)
Destroy 5.00M Cubes
Collect 999i Gold (Total)
Defeat Wave 250 Boss
Get a Team Member to Spec Ops 1 (LVL 1,000)
Shoot Click Pistol 100K Times
Time Warp 10 Times
Collect 999g Gold (Total)
Get 10.0K Critical Strikes
Get Team DPS to 10.0f
Beat Wave 200
Get Team DPS to 10.0e
Destroy 1.00M White Cubes
Destroy 150K Yellow Cubes
Collect 999e Gold (Total)
Destroy 500K Red Cubes
Destroy 500K Cubes
Earn 50.0e Gold
Get Team DPS to 10.0d
Shoot Click Pistol 50.0K Times
Time Warp 5 Times
Destroy 100K White Cubes
Upgrade a Team Member 500 Times
Time Warp 3 Times
Collect 1.00d Gold (Total)
Get Team DPS to 10.0c
Destroy 5,000 Rainbow Cubes
Destroy 50.0K Red Cubes
Get 1.00K Critical Strikes
Get Team DPS to 10.0b
Upgrade a Team Member 125 Times
Destroy 50.0K Cubes
Time Warp 1 Time
Beat Wave 100
Defeat Wave 100 Boss
Earn 250a Gold
Get Team DPS to 10.0a
Get Team DPS to 10.0Q
Collect 1.00Q Gold (Total)
Get 100 Critical Strikes
Get Team DPS to 10.0T
Earn 5.00T Gold
Upgrade a Team Member 50 Times
Beat Wave 50
Shoot Click Pistol 10.0K Times
Get Team DPS to 10.0B
Collect 1.00B Gold (Total)
Upgrade a Team Member 25 Times
Get Team DPS to 10.0M
Beat Wave 25
Earn 500K Gold
Collect 1.00M Gold (Total)
Upgrade a Team Member 5 Times
Destroy 5.00K Cubes
Shoot Click Pistol 1.00K Times
Beat Wave 10
Shoot Click Pistol 500 Times
Shoot Click Pistol 100 Times
Beat Wave 3,500
Defeat Wave 4,000 Boss