Here's what I believe...
Fugitoid reveals that he actually helped to create the Heart of Darkness, either that, or something he says causes the Turtles to loose their trust in him.
The Triceratons intend to destroy Earth just like before, only this time, the Turtles receive aid from all their allies in space - The Salamandrians (Mona Lisa and Sal Commander), the Utroms, The Aeons, The Daagon, and maybe even Tokka.
It is an intense space battle, in the end, the Fugitoid sacrafices himsefl to destroy the Heart of Darkness, just like he did in the 2003 series; and the Team is reuinted with Master Splinter and their friends.
Maybe at the end, Mona Lisa may choose to stay on Earth for a while to see what Raph's home is like.
Once the Space Arc is finsihed, the remainder of the season will deal with the Turtles finding Karai and defeating Shredder once and for all.
That's my theory.