Raiden was captured by the Patriots and used as a test subject for exoskeleton enhancement
Jack eventually escaped that horrible life of war, repressed his memories, and relocated to the United States to join the military. After the events of Metal Gear Solid 2, and with all his childhood memories recovered, Jack was captured by hostile forces during an attempt to steal Big Boss' remains from The Patriots. This was how Raiden was unwillingly transformed into a cyborg ninja, a painful process in which his captors removed his head and spine from his human body and transplanted it into a synthetic one (for testing purposes). Unfortunately for them, he escaped.
As we mentioned earlier, a cyborg body has its benefits, including enhanced speed, strength, and pain tolerance, all of which play a large role in Revengeance's combat. A cyborg body also has its downsides. Rose, Jack's love interest (with whom he had a child), kind of didn't want to date a mostly-robot dude.