Picking up a few months after Batman/Punisher: Lake of Fire,Punisher finds himself back in Gotham (much to his displeasure) and in a firefight with local street thugs while Commissioner Gordon and Co. watch and wait from afar. Punisher whittles down the thugs until he has one left to interrogate: he is looking for Jigsaw. Batman, too, is watching from a distance, but he finally decides to act before Punisher destroys everything and everyone. Batman attacks Punisher, allowing the thug to get away. Batman knows a bit about the Punisher from a distance (since Jean-Paul was wearing the mantle the last time Punisher came to Gotham), but Punisher does not know he is facing a different person under the cowl, thinking the Batman is truly a schizophrenic who changes his fight styles and personalities easily. Despite Batman's grudging acknowledgement they both are loosely out for the same goals, Batman has no desire for Punisher's death-dealing vigilantism in his town, and so he commits to driving the Punisher out of Gotham for good. Punisher escapes in the wreckage during their brawl, leaving Batman to track down what brought Punisher to Gotham in the first place, knowing the Punisher will be there sooner or later.
The thug, meanwhile, has located Jigsaw and tries to convince him he didn't tell Punisher anything about him. Jigsaw is almost convinced, but his mystery partner is not: Joker comes out of the shadows and offs the thug, primarily for a joke. Jigsaw is anxious to make his ascension up the ranks of the Gotham Criminal Underground, having been promised assistance from Joker months ago. Jokes assuages Jigsaw's impatience, urging him to wait until his plastic surgery finishes healing. Jigsaw admits he at least has something to look forward to now that his own nemesis, Punisher, is in town. Joker intimates having an arch-nemesis is the key to making life worth living.
In their respective hideouts, Punisher and Batman research each other, and Punisher can't understand why Batman is the way he is or why they can't get along better since they are on the same team. Microchip is less philosophical, unable to get passed Batman's bat costume; Batman is likewise unwilling to probe the situation too deeply, seeing only the potential damage having a death-dealing vigilante in town could due to Gotham. Microchip and Robin figure out the main conflict is the gang authority situation, causing Batman to wonder who could gain from another gang war.
Punisher and Batman follow the path up the crooked ladder to a meeting of major criminals, while Microchip and Robin fight each other digitally over the computer network they are both trying to hack. Jigsaw recognizes Punisher, escalating the conflict faster than either Punisher or Batman anticipated, but Punisher doesn't mind getting to the explosive finish sooner rather than later. Joker, too, appears quickly, aggravating many of the high-ranking criminal bosses who want nothing to do with him. While the gangs start shooting each other up, Joker delights in the carnage as Batman does his best to end it quickly without loss of life. Punisher, though, has no such qualms, which endears him to Joker. In the melee, Jigsaw's face gets torn up again. Batman confronts Punisher and demands he get out of Gotham as soon as this fight is over, ignoring Punisher's attempts to make a truce. They "change partners" (as Joker says) and Batman takes out Jigsaw while Punisher goes after Joker. Joker points out Punisher and Batman have even more in common, since they both lost their families long ago: Joker deduces Batman lost his family long ago since he reacted like a child would (costume, toy gadgets).
Jokes slips on a banana peel as Punisher closes in on him. Joker realizes too late the Punisher actually will kill him, apparently having grown accustomed to the fact the Batman does not kill. Just as Punisher is about to pull the trigger, Batman prevents him and tells the Joker to run for his life. The Punisher is incensed at Batman's willingness to let his nemesis go when he could have ended his madness once for all. Punisher hits Batman in a two-page splash, which Batman shrugs off, letting Punisher think he deserved that one. Batman prevents him from landing another punch and reiterates his threat to put him away if he ever returns to Gotham. Punisher is incredulous, declaring he and the Joker deserve each other. Frank is eager to get back to his own "cesspool," NYC, where at least things make sense (unlike in Gotham City). "I hate Gotham," thinks Punisher, on his way out of town.