The last days of Cable's time with the Six Pack is told; it is mirrored by a mission he and Kane go on to find Stryfe.
The Present: Having convinced Garrison Kane that he isn't Stryfe (and having promised to help Hammer in exchange for Kane's assistance), Cable and Kane head to Japan to see if they can intercept the Mutant Liberation Front before they can get to the last artifact. Upon entering the Yashida ancestral home, the men are jumped by a swarm of ninjas. They go to work but Kane is soon subdued. The new Silver Samurai appears and begins to take a swipe at Kane's head. He stops when he realizes that Cable has put a gun to his head. Cable proposes a deal: let them switch out the antique for a fake. They'll place a tracker on the fake so as to find Stryfe. Silver Samurai gets the pleasure of being owed a favor. The deal is agreed to and Cable and Kane leave.
Seven Years Ago: Face-to-face with Stryfe below the opium route, Cable chucks a string of explosives at Stryfe. Stryfe easily teleports out via Zero and Cable bodyslides his team out before the explosion. Stryfe's grunts aren't so lucky. The Six Pack is furious. They'd never broken a contract before. Cable says the contract doesn't matter anymore - Stryfe is there and acts as a constant threat.
The Present: Stryfe meets with his antique specialist in Mexico and is told that the mask from Japan is a fake. Stryfe is furious and threatens to kill the specialist, a Mr. Richter. Richter asks if he is going to be killed like his brother was killed simply because Stryfe didn't like hearing the truth. Stryfe lets Richter go and Richter informs him that a device was found on the mask, a device that had never been seen before. Stryfe recognizes the signature of the device and realizes that Cable is on his trail.
Sure enough, Cable is watching the progress of the trace and learns that Stryfe is in Cancun. Kane walks in and asks a pretty deep question: does Cable ever regret decisions from his past? Cable replies that he makes decisions based on what is best at the time and only thinks on their appropriateness later. Angered, Kane rips off his shirt to reveal his metal arms and asks if Cable regrets the decision that forever scarred Kane? Cable states that he'd make the same decision.
Six Years Ago: With Tolliver angered at the Six Pack for breaking their contract, mercenaries from all over are trying to take the team down. In Singapore, the Six Pack is trapped at a bridge. Domino dives underwater and plants a bomb that completely takes out the opposition. The team moves on and Cable asserts that they aren't out to get Tolliver but Stryfe. The team wonders why they should trust Cable. He simply says because he's asking them to.
The Present: Cable and Kane march through some Mexican jungle to an ancient fortress. Before they can enter, however, a large part of the building falls. This acts as a distraction for the MLF, as they try to take the men unawares. Cable uses some of his teke abilities to take them out. Inside, however, they meet a much larger reception of MLF forces. Before any fighting can begin, Stryfe appears and, once again, takes Kane hostage. To further complicate matters, Stryfe removes his helmet to show Cable that, indeed, they share the same face.
Six Years Ago: The Six Pack find a Stryfe installation in Uruguay. They infiltrate the base and Hammer downloads a ton of information onto a disk. The team rigs the place to explode but are unable to leave due to Stryfe's intervention. He teleports in and takes Kane hostage. He proposes a trade: the highly valuable disk for Kane's life. The team tries to fight Stryfe, but it is no use. Hammer gives in and starts to approach Stryfe with the disk. There isn't much time left on the charges so Cable does the only thing he can think of - he shoots Hammer in the back to retrieve the disk. Stryfe, however, is able to use his own teke abilities to grab the disk and teleport out. Seconds before the bombs explode, Cable bodyslides out and leaves his team to fend for themselves. Hammer and Kane are severely hurt while Domino, Grizzly, and G.W. Bridge are able to find safety.
The Present: Cable finds himself in the position. Stryfe wants the data-link to Cable's computer for the life of Kane. Cable shows the disk and Stryfe lets Kane fall to the ground. Cable then incinerates the disk. Stryfe is not pleased. He hits Cable with a huge burst of energy that threatens to tear Cable apart. Kane nails Stryfe with electrical currents from his arms and stops the skirmish, but no one is able to finish the fight. Cable wishes he could finish Stryfe then and there, as he's lying in a heap, but Cable also recognizes the need to get Kane some help, as the boy is barely holding on. Cable timeslides to the future.
Kane awakens to find that he's been repaired by way of the technologies of the future. Looking at the futuristic skyline, Cable assures Kane that if he had to do it all over again - saving Kane or killing Stryfe - he would have done things the exact same way.