Unfortunately Snake and Raiden’s mission to rescue Olga’s daughter didn’t exactly go off without a hitch. His relationship with Rose started to experience problems due to his resurfaced memories of his past, and she seemed to have lost the baby. For some reason, she also married Campbell, whose AI she was teamed with during the Big Shell incident.
Eventually, Raiden’s knowledge about the AI became very useful to Big Boss’s former comrade Eva-the surrogate mother of Solid and Liquid-who was keen to get back the body of the legendary mercenary….and her former lover. In exchange, she gave his resources to find Sunny. The mission was a success, although Solid Snake largely stayed behind as a strange aging illness-in fact his clone termination genes activating-began. Snake and Otacon largely took care of Sunny aboard their floating jet, the Nomad, although Raiden remained good friends with the girl.
Working with Big Mama and her “Paradise lost” army, Raiden-after learning many tracking skills and refining his use of a high-frequency blade-went to find Big Boss’s body, a possible genetic key to getting into the Patriot’s AI network. However, he was captured by the human agents Patriots, and much like Grey Fox before him, became a test subject for cyborg technology. Eventually rescued-and treated by Dr.Madnar (Possibly the same man who had helped Big Boss develop the Metal Gear in Outer Heaven and Zanzibar Land), he nevertheless was a changed man. Gone was the naive agent and pawn; in it’s place, a Cyborg ninja.
Raiden re-joined Snake in South America during his attempt to find Liquid Ocelot, helping cover his escape after rescuing Naomi Hunter.
Here, he held his own against a series of GEKKOS (Mass-produced war machines based on Metal Gear technology)-and old enemy Vamp, who was working with Ocelot’s Outer Heaven group after escaping from the Big Shell.
Raiden’s new body was injured in the fight, and took some time to recover. Somewhat discouraged, Snake gave him some encouraging words, yet again.
Raiden: “It was never going to work out for me. It even rained the day I was born.”
Snake: “You’ve got it all wrong. You were the lightning in that rain. You can still shine through the darkness.”
After his recovery, Raiden then helped Snake at Shadow Moses, once again fighting Vamp for one last time (Vamp was later finally destroyed by Naomi disabling his nanomachines) and helping Snake clear the way when he commandeered Metal Gear Rex.
However, at the end of the mission, Raiden was badly crushed not only by boulders, but by the battleship Outer Haven. As he appeared to have finally been crushed, he cried Rose’s name.
However, that still wasn’t the end for Raiden. Although he had lost his cyborg arms for the time being, he still had enough left in him to help Snake when he boarded the ship, fighting off a group of HAVEN troopers with his sword in his mouth.
After the whole inciddent was over Once again recovering-but with a noticeably more human like jaw-Rose visited him in recovery, where he learned the truth-Rose hadn’t married Campbell, it was all another ruse to fool the Patriots.
Not only that, but she had given birth to a son, John, who thought it was cool that his father was a ninja, thinking he was kind of like a comic book superhero.
But Raiden’s story has at least one more tale, although he exited the saga of the Snakes.