Spoiler!
There are 2 systems. The bad system is with the senior guy and the good one is with eden. The bad system tries to control them by deleting different parts of their memories(including the senior guy and eden) and throwing them in a regression loop with them getting crushed at the end each time and the good system is trying get eden out of this loop but the pre-regression eden had the bad system (that doesn't even remember he had one)
Enhaforlife