The team came about after all three members had run ins with the Punisher that ended badly for them. Daredevil was defeated by Frank Castle tied up and forced to choose between killing the Punisher or a mobster with a gun the Punisher gave him only to find out it was empty. Spiderman encountered the Punisher saving his life when he was thrown off the empire state building by the Russian. Spiderman ended up getting knocked out by the Russian and even though he saved the Punisher's life Frank used Spiderman as a human shield to defeat the Russian. Wolverine had his genitals shot off by the Punisher when they were chasing after the same killers. The Punisher than ran him over with a steam roller stating Logan was just getting in his way. All three have grievances with the Punisher and want to bring him to justice.
The Confederacy of Dunces team was created by Garth Ennis during his Punisher Marvel Knights run. Garth Ennis used them to show off his black comedy writing that he is famous for and his general dislike of superhero comics.
Major Story Arcs
Confederacy of Dunces
Daredevil gathered Wolverine and Spiderman together where the three reflected on what the Punisher had done to them all. Daredevil wanted their aid in bringing Frank Castle to justice. He didn't want Frank Castle dead since he didn't want them to be like the Punisher. Spiderman agreed to help take down the Punisher Wolverine wanted him dead but in the end agreed to Daredevil's proposal.
The three used a snitch that the Punisher didn't know they also shared and lured Frank out. The plan was if Castle didn't come along peacefully to overwhelm him. The Punisher upon realizing the three of them set up an ambush for him and that he was going to lose if he tried to take them on right there and then didn't fight them. The Punisher stated that he was in the mood for a cheeseburger since prison food was horrible. Frank then handed over his shotgun to Daredevil and went into the diner behind them with Spiderman, Daredevil, and Wolverine to dumbfounded by Frank's actions to stop him from doing so.
The Dunces follow the Punisher into the diner where he is sitting calmly ordering a cheeseburger and about to confront him when Spacker Dave who has been following the Punisher all day as part of his "super-spotter" hobby interrupts them. Dave wants is asking them questions and distracting Daredevil who is trying to get Dave to leave the restaurant. Spiderman and Wolverine are watching the Punisher when the waitress comes over to them annoyed and asks if they are going to order anything. Spiderman orders some coffee to satisfy the waitress which leaves the Punisher and Wolverine alone. The Punisher realizing the other two are distracted proceeds to elbow wolverine in the face breaking his nose which enrages wolverine. Daredevil and Spiderman then have to stop Wolverine who is in a berserker rage from killing the Punisher. Finally Daredevil manages to subdue him only to find out the Punisher escaped in the chaos.
The Punisher realizing the three are after him plans to give them a reason for not following him anymore. The Punisher grabs an ex convict and butchers him in Hell's Kitchen which he knows will draw Daredevil and the other dunces. Daredevil hears the noise while he, Wolverine, and Spiderman are looking for the Punisher. The three of them arrive to find the man dead and gutted with a not pinned to his chest. Wolverine goes over to see what the note says. He grabs the note and sees that it says "suckers" Wolverine says the word out loud not getting its meaning just as Frank Castle across the street in another building fires a rocket launcher at him blowing him up. Spiderman reaches where Frank Castle was before Daredevil and enters the room he was standing with his foot going through a floor board. Castle casually flicks on the lights to reveal dozens of mines in the room all pointed towards Spiderman. Peter doesn't dare move since he knows he will die if he does.
The Punisher than races out of the room preparing to deal with Daredevil, Daredevil surprises the Punisher though and starts beating up on Frank. Castle desperate tackles Daredevil out the window where Daredevil barely manages to grab onto a railing dislocating his shoulder. The Punisher hanging on to Daredevil pulls down with all his weight dislocating Daredevil's other shoulder which causes daredevil to fall onto a fire escape head first. The Punisher proceeds to warn Matt not to come after him again and then proceeds to leave. Even though Frank knows they weren’t going to stop coming for him.
After, a few days pass and everyone had a chance to heal up from the last encounter Frank calls Matt at his law office to tell him he is ready for their final show down. The Confederacy of Dunces arrives to find Castle calmly waiting for them. Frank offers them all one last chance to give up their quest of taking him in. After they refuse to do so and tell him to do his worst Frank tells them "It's not my worst you have to worry about." The Punisher then jumps into an open manhole cover and three are about to go in after them when they hear a loud roar. The building behind them then explodes and they see an enraged Hulk coming at them. The three try to stop the Hulk with Wolverine going at him head on. The Hulk hits Wolverine which sends him soaring through sky out of the fight. The Hulk then hits the ground with his fists trying to smash Spiderman and Daredevil with them both barely escaping certain death. Daredevil didn't get far enough out of the way and falls into the sewer with rubble on top of him immobilizing him with the Punisher looking right at him.
The Punisher explains to Daredevil that he found the Hulk at a mob auction where they were trying to sell him to the highest bidder. Apparently Bruce Banner had amnesia. So Frank knowing that the Dunces were after him saved the Hulk to use against them if they would not abandon their mission to stop him. Daredevil outraged tells Castle they have no way of stopping the Hulk and being in Brooklyn the damage and deaths he would cause would be on his hands. The Punisher then informs Daredevil that he has been feeding the Hulk C4 for the past eight days and proceeds to pull out a detonator and press its button which causes the Hulk to howl in pain in revert back to Bruce Banner. The Punisher informs Daredevil for the last time that locking him is useless since he will just kill everyone in prison and that there is only way to stop him and unless he is ready kill him he is just wasting his time. The Punisher than leaves Daredevil in the sewer and the Confederacy of Dunces disbands giving up their quest to put The Punisher behind bars.