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