Raiden began living together with Rosemary, but the tragic memories of his days as a child soldier started to resurface, causing tension in their relationship and leading him to leave her.

Raiden learned that Olga's daughter, Sunny, was being held in Area 51.

He successfully rescued Sunny with the help of the anti-Patriots resistance group, the Paradise Lost Army.

After hearing of Rosemary's miscarriage and subsequent remarriage to Roy Campbell, Raiden became despondent. He left Sunny in the care of Hal Emmerich and Solid Snake, then began work on retrieving Big Boss's remains from the Patriots for the Paradise Lost Army, leading to his capture.

As a prisoner, the Patriots used Raiden as a subject for experiments in exoskeletal enhancement surgery.

Raiden was treated as a test subject in the Patriots' research into creating the Perfect Soldier, just as Gray Fox had been made into the enhanced and heavily drugged Cyborg Ninja before him.

With help from the Paradise Lost Army, Raiden managed to escape his captivity. After undergoing surgery to clear his body of nanomachines, he was successful in reclaiming Big Boss's remains from the Patriots. The enhancements implanted throughout Raiden's body, however, were too severe to allow him to live again as a normal human. He elected to disappear from the life of his fiancée, Rosemary.

Left to wander the earth, Raiden studied scouting techniques under a Native American shaman living in Alaska, also learning to hunt.

Upon receiving orders from Big Mama to assist Solid Snake and lead him to the Paradise Lost Army, Raiden set out into battle once more.