When 80s Shredder and Krang appear in the 2012 dimension, they employ Bebop and Rocksteady and find their plans are succeeding better than ever. Meanwhile, the Turtles try to adjust to life without serious bad guys.

The Turtles must train their 80s counterparts into fighting like real ninja. The 80s Turtles begin to learn the difference between their world and the world of their modern counterparts.

The Turtles, their 1987 counterparts, April and the Mighty Mutanimals must work together to stop 80s' Shredder and Krang from destroying the world. Meanwhile, Bebop and Rocksteady are faced with a difficult and life-changing decision.