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