John was an agent for the NSA who's job was to infiltrate the
and report on the experiments that
finds dead drops that were left by John before the beginning of the game, detailing what was happening inside the First Sons in relation to the
and his opinion of the situation. Through the audio logs, it is revealed that John was
's handler and worked under Kessler. Before meeting with John, Cole is in contact with someone who is claiming to be his wife, named
. When Cole meets up with John, he states that he never heard of her and to cut all communications with her. After meeting for a second time, they join forces to find the Ray Sphere. When the two have found the Ray Sphere, you can choose to destroy it or use it to enhance your powers. Regardless of the choice made, John ends up dying.
John makes a few postmortem vocal cameos in
, in pre-recorded conversations with fellow NSA agent
. Nearing the end of the game, however, it is revealed that John is in fact alive, and is the embodiment of
that Cole has been preparing for for so long.
John was found to be a Conduit, which when combined the explosion he suffered from the Ray Sphere in inFAMOUS, awoken his powers. At first he was just a mess, and was scrounged around everywhere; but his own will managed to slowly, and painfully, piece himself together across the months until he finally reawakened nearing the beginning of inFAMOUS 2.
He was still disorientated, however, and could still only act on impulse through the pain which forced him into his massacre and destruction of Empire City. Nearing the end when he shows himself to Cole, he shows the severity of the plague that was afflicting Empire City and how as taken hold in New Marais (which is also insinuated that it's being spread by Cole) through a new power. John, now in complete control of himself, also shows how Cole cannot heal the plague with his powers, but John himself can heal fellow Conduits who haven't had their powers awakened. Through that revelation, it forces Cole into an ultimatum to either help John finish his goal of using his powers to heal all the Conduits, but which will destroy all of humanity--as that's what John believes is the worlds only hope--or carry on his mission to thwart The Beast and place hope on the statements from Sebastian Wolfe that the Ray Field Inhibitor will be able to cure the plague for all of humanity.
Cole will abide by his original promise to stop The Beast, and with the help of Nix, Zeke and Laroche will use the power of the RFI to stop the beast - all the while knowing it'll kill every Conduit in the world through the process. Kuo didn't agree to those terms, however, and ran off in fear to aid John.
Even with all of the blast-cores, the RFI wasn't fully charged. Fortunately, Zeke came up with an idea to use substation placements through New Marais to give it the final douse of juice it requires. Cole meets up with Laroche to head to the first one near the bridge separating the two islands of New Marais, only to find The Beast awaiting them having already destroyed the substation. Laroche and a great deal of his rebel army will perish as Cole frantically manages to escape to the second, along with Nix.
They place the RFI in the substation, with Nix stationed as defense. The Beast will soon follow forcing Cole to once again engage the monstrosity. Kuo also makes a few sporadic appearances to thwart Cole, but is bested every time. Midst Cole using an Ionic Storm on The Beast, the RFI's substation will be finished, though it still hasn't reached full power yet. In order to bide Cole some more time Nix sacrifices herself allowing Cole the space to carry on towards the cathedral. Here Cole will place the RFI in the substation giving it complete power. As The Beast draws near Cole will barrage him with rockets, weakening him further. At this point a battered Kuo also arrives and admits defeat, along with her fear of dying. With everything in check Cole finally releases the power of the RFI which spreads a world-wide blast, killing all Conduits but healing all regular humans of the plague.
The epilogue proceeds with Zeke narrating about the events, and shows how the once misunderstood Demon of Empire City was graced as a true Hero and was given a monument placed in New Marais with his Amp laid the tombstone. Cole himself is buried at sea by Zeke.
Here, Cole will toss aside his original mission and, along with Kuo, leaves to aid The Beast. Upon arriving, the power is shut down across the city. But The Beast will share some his own power to allow Cole permanent flight as long as he in close vicinity. As the two travel across the city, Nix will arrive to oppose the two. Equipped with the RFI, she attempts to hold off The Beast's attacks, but is killed by Cole soon after. The RFI will drop from her hand and roll over to Zeke. Zeke admits he has no chance but tries anyway for the sake of standing up for humanity. Cole himself is still a little reluctant, but kills Zeke in the end regardless.
At this point, The Beast is struggling with his own mortality and cannot bear with all of the death and destruction. He still stands alongside his ideals, however, and transfers his own incredible power to Cole so he may carry on their goal.
The epilogue shows Cole using this new found power to unleash a Ray Sphere blast which completely decimates the city of New Marais. It does, however, do much as John predicted and awakens all of the Conduits. From here they all march across the world with Cole leading the way, massacring all resistance and releasing more Ray Sphere blasts. He narrates that he declares this as the latest stage of evolution, with himself, the new Beast, charging his way forward.