Some TMNT stuff really isn't for little kids.
After Splinter and the Turtles were transported to Batman's dimension, Casey was sent after them in an attempt to rescue them. In addition to five canisters of mutagen, Harold Lilja equipped him with a "slingshot" that would allow him to transport himself and his friends back to their universe.
However, Shredder and Ra's al Ghul assaulted him and took the mutagen. Additionally, the Turtles were unwilling to leave Batman to certain death, even if it was at the cost of their own existences. Casey transported back without them, but returned a short time later with April O'Neil through a dimensional portal, putting themselves at risk to do so.
When Bane invaded New York, Casey helped Leonardo, Raphael and Michelangelo attempt to quell the chaos. While Leonardo, Splinter and Batman went to spy on Bane, Casey remained behind with the other Turtles and Robin, and witnessed a fight between Robin and Raphael.
While Batman, Robin, Splinter and the Turtles were infiltrating a Foot Clan lab, Casey remained on the radio to keep tabs on them. He remained with April as she established contact with Batman's dimension, and wished Raphael luck as his friend took the wounded Splinter to the Lazarus Pit. Upon their return, he greeted Batgirl.
In the final battle on Liberty Island, he helped April free the imprisoned humans and lead them to the ferries. Before the superheroes returned to their own dimension, he posed with them and the Turtles in a photo taken by April.