Hydra was working on a device that could give or cure various different diseases by re-writing a person's biological make-up. Agent-X was hired to get rid of the machine, but it was tested on him during his assault on the headquarters and he was given severe artritis. Because the artritis is now genetically a part of him, his healing factor won't get rid of it.
Sandi and Outlaw contacted (the still 3-inches tall) Deadpool to rescue Agent-X, whom at this point had been missing for 2 or 3 weeks... Deadpool would only do it if they flashed him, so Deadpool and Weasel found the Hydra headquarters Agent-X went to.
Deadpool broke in and threatened (and applied) a weak-willed Hydra member with bodily harm in order to help get to where he needed to go quickly... meet Bob, Agent of Hydra. Deadpool and Bob found where Agent-X was being kept, and behold... Agent-X is about 800lbs.! Turns out that Hydra gave Agent-X an eating disorder to keep him occupied.
During the fight with Hydra, Deadpool returned to his normal size. He, with Bob and Weasel, got Agent-X out of there on one of Hydra's planes. They used the machine to take away Agent-X's eating disorder, but he had a problem... it was going to take Agent-X a while to get back into shape and he had alot of bills to pay, so he couldn't afford to take any sick days. So he made Deadpool an offer... Deadpool is now in temporary control of Agency-X!
Meanwhile, back at Agency-X, Sandi and Outlaw have been taken hostage by T-Ray who's out for not only Deadpool's head, but Agent-X's too!