What If the Punisher Had Become an Agent of S.H.I.E.L.D.? starts with Nick Fury and S.H.I.E.L.D. having the Punisher cornered. Nick Fury gives him a choice, work for S.H.I.E.L.D. or be thrown in jail. The comic diverges from canon, when the Punisher accepts Fury’s offer to became a S.H.I.E.L.D. agent. He rationalizes that he could take down even bigger villains working for them.
Frank is rewarded with his own squad of soldiers to direct. One of his first missions is to bring in Yellow Claw for interrogation. It all goes accordingly to plan until Frank executes Yellow Claw at point blank range. Nick Fury is furious with the Punisher for not following protocol. His next mission is to bring in some drug lords. Frank brings them in but only after torching their whole operation. Fury outraged again, demotes Castle to Chase Unit Zed.
On his next mission, Dum Dum Dogan is the head officer. They are ambushed by Hydra agents and everyone but Frank is killed. Unbeknownst to them, their locale was a secret Hydra base. Frank managed to avoid detection on the island for three weeks. With S.H.I.E.L.D. presuming he is dead, he is free to go back to being the Punisher.
The Punisher has Microchip hack into S.H.I.E.L.D.’s database for infromation on Hydra Island. He then hijacks a S.H.I.E.L.D. plane by using his old access code. Vowing revenge for the fallen S.H.I.E.L.D. agents, he charts a direct course for Hydra Island.
Upon arrival via a SH.I.E.L.D. flight suit, he is greeted by hundreds of Hydra troops firing upon him. He starts killing them left and right but gets hit a few times along the way. The Punisher makes it to their nuclear power plant and sabotages the core. As it begins to go critical, he attempts to make an escape but is too outnumbered. As he starts to die, he thinks about his family and how has war has finally come to an end.