Question about Metal Gear solid 2s plot connecting to MGS4 (spoilers)

Well I didn't know which forum to post this in, but whatever.

Exactly how does Raiden turn into a cyborg in MGS4? I just replayed MGS2 and I just realized I have no idea how that happens. Are there more then 1 endings?

My memory might be failing, but I think Raiden was looking for Sunny in Area 51 (the confidential government facility) and he was taken by The Patriots, whom made him into a cyborg.

Taken from the MGS wiki's article on Raiden...

"Raiden learned from Big Mama, in exchange for the location of Big Boss that he obtained from GW, that Olga's daughter, Sunny, was being held in Area 51, and successfully rescued her with the help of Big Mama and the Paradise Lost. After hearing of Rosemary's miscarriage and subsequent remarriage to Roy Campbell, Raiden became despondent. He left Sunny in the care of Otacon and Snake. Afterwards, he left to wander the Earth. Raiden studied scouting techniques under a Native American shaman living in Alaska, and learned to hunt. He 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 test subject for experiments in exoskeletal enhancement surgery, during which he had his head and spine excised from his body from his lower jaw down and subsequently grafted into an enhanced synthetic body.

With the help of the Paradise Lost Army, Raiden managed to escape his captivity. After undergoing surgery to clear his body of nanomachines and being saved by Dr. Drago Pettrovich Madnar, 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 a normal life again. He elected to disappear from the life of his fiancee, Rosemary."

...Ouch.