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