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