Having heard of robberies at S.T.A.R. Labs, LexCorp and Powers Industrial, the Penguin decided to steal experimental tech from Wayne Enterprises so that he could then sell it to Shredder. Before he could enter the Wayne Enterprises building, the Turtles began attacking his men from the shadows. He initially believed them to be Batman, but upon seeing the giant Turtles for what they were, ordered his men to kill them.
When all his men were defeated, the Penguin opened fire with his weaponized umbrella, temporarily driving the Turtles back. Leonardo disabled it with a shuriken, only for the Penguin to attack him with a retractible blade in the umbrella. When defeated again, he leaped off the building and flew away with a propeller in his umbrella.
He was later hired by Ra's al Ghul to obtain a cloud seeder that Batman had hidden on a Wayne Enterprises cargo ship. Upon delivering the device, he expected payment from Shredder, only to be told that there was no money. Realizing he had been tricked, the Penguin ordered his men to kill Shredder, only to see that the Foot Clan had executed them all a few seconds before. Realizing that his only other option was death, the Penguin chose to leave without payment.