Well, it was all a dream!! Ok, sort of. This was such a tedious movie I'm just glad I didn't see it at the cinema.
So Remy grows a conscience after his op and can't kill anymore. He has been kicked out by his wife, but that's ok because he soon enough gets together with the singer he met before, who happens to be now a homeless junkie full of fake organs.
Remy tries to change his account online back at the office, but finds out that it can only be done now at the factory. They try to flee the country but are found out at the airport, and then chased by Jake. After they get a dodgy doctor to fix Beth's knee, Jake finds them and lets them know that he fixed the defibrillator to keep his friend working. Remy is knocked unconscious again - and sees his life flash before his eyes.
Beth rescues him and their hideout is hit by the Union. A lot of people are zapped, but they make it out ok. Remy is now determined to bring down the Union, so they get into the Factory - and then Remy forgets his oath and kills a ridiculous number of guards and staff personnel Matrix-style. They get into the main scanning room and delete records for all the body parts.
Jake kills Liev Schreiber, and then helps them blow up the scanner.
It cuts to Remy on a lounger at the beach, waited on by Beth, next to his pal Jake. The scene flickers, and then we're back to when Remy was last knocked unconscious. Jake feels bad, so has paid for his old friend to be part of the neural dream science unit (Vanilla Sky style), leaving Beth behind alone, still knocked out cold.