Time is recorded separately for each chapter of the game and you are permitted to retry individual chapters to improve their time. Pausing the game will pause the timer. Choosing the 'restart chapter' option from the main menu will reset the timer for that chapter. Loading a checkpoint (either by choice or by dying) or loading a quicksave will not reset or stop the timer.
The achievement will be unlocked as soon as all Mudokons in all chapters have been saved and the game's overall recorded time drops to or below 3:00:00.
These times are targets you should roughly aim for in order to get the achievement.
RuptureFarms Escape 00:17:07
Stockyards 00:16:30
Monsaic Lines 00:03:43
Paramonia 00:08:28
Paramonian Temple 00:15:16
Paramonian Nests 00:01:18
Scrabania 00:16:22
Scrabanian Temple 00:19:11
Scrabanian Nests 00:02:34
Free-Fire Zone 00:04:59
Zulag 1 00:21:30
Zulag 2 00:09:36
Zulag 3 00:10:03
Zulag 4 00:09:37
Boardroom 00:02:09
Total Time 02:38:23