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