Shredder made an alliance with Ra's al Ghul and the League of Assassins, out of his desire for the immortality granted by a Lazarus Pit. In exchange for the Pit, the Foot Clan would provide mutagen stolen from T.C.R.I., and a means of spreading the substance over the entirety of Gotham City. To this end, Shredder stole the mutagen, and then went to Gotham to build a mutagen-disseminating device.
The Turtles followed him to Gotham, but were unable to stop the Foot Clan from stealing equipment from S.T.A.R. Labs, LexCorp and Powers Industrial. When the Foot attempted to steal a cloud seeder from Wayne Enterprises, they were unexpectedly thwarted by Batman, who defeated all of Shredder's ninja before fighting him individually. The superhero seemed to have the upper hand until Shredder attacked him with the sato oshi strike, which badly injured Batman and briefly exhausted Shredder.
Tensions began to rise between Ra's al Ghul and Shredder because of this setback, and Shredder demonstrated the effectiveness of the mutagenic ooze by having Baxter Stockman inject a League ninja with it. He then went to Arkham Asylum with Ra's al Ghul, where the two killed the entire security staff.
Shredder was displeased by this particular venture, believing it to be a waste of time they could be using to get the cloud seeder, and disdainful of the "freaks" imprisoned in Arkham. However, after Ra's al Ghul had obtained the Joker Venom formula from the Joker, Shredder paid the clown with a canister of mutagen.
The Joker's subsequent actions served as an effective distraction for the Turtles and Batman, during which time the Penguin obtained the cloud seeder and delivered it to Ra's al Ghul and Shredder. When ordered to deal with the Penguin's compensation, Shredder confirmed that there was no money to pay him with, even as the Foot executed Penguin's followers. He threatened to kill the Penguin as well if he did not leave.
Shredder and Ra's al Ghul then fortified themselves in Ace Chemicals to finish building the device, and mutated a number of both League and Foot ninja to protect the building. However, the Turtles and Batman managed to break through and engage their enemies, with Batman determined to have another opportunity to fight Shredder after his previous defeat.
Shredder was an effective foe for Batman, fighting him on equal footing and even seemingly defeating him. As he prepared the sato oshi strike once again, Batman temporarily confused him by saying "Cowabunga," allowing Raphael time to slam into Shredder's head, knocking off his mask. Batman then attacked Shredder again, punching him repeatedly until Shredder's face was bloodied. He stated that the League and the Foot were his, and that his enemies had no way of stopping him.
As he spoke, the flaming remains of the mutagen-disseminating device fell through the ceiling, throwing Shredder into a vat of chemicals. The Ace Chemicals building then collapsed and exploded, seemingly killing him. However, Leonardo cast doubt on the idea, pointing out that Shredder had seemingly died before.
Leonardo's supposition was proved to be correct, as Shredder later crawled from the remains of the Ace Chemicals building. However, the chemical exposure had caused him to become a duplicate of the Joker.
- The claw marks on Shredder's face are presumably a homage to the 1990 movie, in which Splinter's attack had left scars on his enemy's cheek. However, the origins of these scars are not explored in the crossover.
- His appearance overall is a blending of his 1990 film (red clothing and scars) and 1987 series counterparts (helmet design and purple cape).