In an alternate future, where Ch'rell ruled Earth, Baxter Stockman's brain was attached to an aged, wheelchair-bound Hun. Stockman designed Shredder's suit and made it to be unbeatable, which he later came to regret. At some point, Baxter was attached to Hun by Ch'rell as a punishment. In 2029, Stockman and Hun were to be executed but were saved by the Turtles resident to that alternate reality, and April O'Neil, joining the rebellion against Shredder and using his tech knowledge to assist.
In 2034 Baxter came to meet Donatello, who had years ago been displaced by Ultimate Drako, Baxter commenting Don looked younger then ever. During the an attempt to overthrow the Shredder. After sufficient motivation, the team decided to attack Ch'rell's palace. A captured Karai Legion that had been modified by Stockman was used and enhanced by Donatello for the confrontation.
Baxter and Hun were supposed to stay in the Turtle Tunneler. However in the confrontation with Shredder to Baxter's shock and horror, Hun attempted to betray the rebellion, left the Tunnel and ran up to Shredder, begging him to take him back. Ch'rell said that this was the perfect chance to finish the two traitors and stomped on Hun, due to lack of locomotion, Baxter was killed as well by Hun's error.
While Baxter had died, his contributions would allow Donatello to finish off Ch'rell, thus avenging Baxter and the Rebellion.