Perfect Agent is tough. You're going to need a lot of determination to finish the game on Perfect Agent. Refer to "Completed Single Dark Agent" for tips.
There is a checkpoint in five of the missions on Perfect Agent difficulty. The location of the checkpoints are as follows:
Just after you blow the CPU core with the CamSpy and the cutscene ends, you'll pass the checkpoint.
Grab Zeigler's briefcase in the safehouse and you'll clear the checkpoint.
You'll pass the checkpoint upon reaching the final battle against Killian's Dropship at the docks.
Upon reaching the deathmatch fight against Mai Hem you will be given a checkpoint.
Reach the final battle against Mai Hem to pass the checkpoint.
Complete all 14 missions on Perfect Agent, (or a higher difficulty) in single player, to unlock this achievement.