Although the two fought from time to time, they never did really go into the elephant in the room: Deadpool was an experiment based around synthesizing Wolverine’s healing factor. He wasn’t quite a clone, but an attempt to recreate Logan in a non-mutant form. They finally delved into this in the pages of Wolverine Origins, where Deadpool went full Chuck Jones with various cartoonish Wolverine traps until finally capturing his prey.
With Wolverine as a captive audience, ready to be killed, Wade laid out his bitterness. Wolverine is this handsome hero with a team full of people who love and respect him. Despite this, Wolverine is a gruff asshole who spends his time trying to get revenge on those who wronged him. Meanwhile, Deadpool is a hated, ugly loner who is a freak among freaks. He’s not allowed to join the X-Men because he’s not really a mutant, making him a man without a country. Bitterly looking at his scarred reflection and then tugging his mask down, Deadpool grumbled, “I’m the one who should be out for revenge…”
Deadpool would force himself onto the X-Men team a couple times, very much against Wolverine’s will. During one such time, Deadpool was widely hated due to the false belief that he tried to help Skrulls take over Earth months. Deadpool secretly knew that he could never truly work as a member of the X-Men and played the team, making himself look like a crazed villain who needed to be beaten down by the mutant heroes. He used his own rotten reputation to make the X-Men look so much better to the public eye for stopping his scheme.
Then came Uncanny X-Force and the moment where things truly changed. At the time, X-Force was the deadly black ops team that the rest of the X-Men didn’t know about else they would have moral disputes over it existing. Deadpool was part of the secret team, hired by Archangel. One mission involved them having to hunt down a reborn Apocalypse. To their surprise, the new Apocalypse was in the form of a child. With the team questioning how to handle the situation, Fantomex coldly took action and shot the young mutant in the head.
Sometime later, Deadpool called a team meeting, not because of any special missions on the agenda, but because he was having a hard time dealing with Fantomex’s actions. He did not sign on to murder children. Wolverine tried deluding himself into believing that it was for the greater good and did so by dressing Wade down for being a soulless, greedy, piece of shit. Deadpool acknowledged that and added, “Yeah. But I never killed a kid,” before storming out.
To Wolverine’s complete shock, Archangel then told him that after over a year of employing Deadpool, Deadpool never once cashed any of his checks. He was not doing this for money, but for the chance to do right.