Okay so this happens after Mikey has been with Splinter and April healing. His brothers are going crazy trying to find him and get him back. (Leo has begged Miwa several time to let his brother go [its a complicated story but the Shredder told the turts that Splinter is keeping Mikey prisoner])

Finally Mikey is well enough to walk and goes to stop his bros (who have been beyond reason and have been pretty merciless while fighting April, Casey and Miwa) and when Mikey shows up, they are locked in another battle.

(A little something of the scene I drew):

“No, stop!”
Leo froze, he knew that voice like he knew his heart. 
Leo turned his head to find the source of the voice, searching like he had been for months. 
There through the fog and the darkness was his little brother. 
Missing his prosthetic, but uninjured and looking well rested for a change. 
“Mikey!” Leo’s face lite up, Miwa and the fight forgotten, he ran as fast as he could to his lost brother. Placing a hand behind Mikey head and bringing their foreheads together. 
“Your alive! Your okay”
“It’s so good to have you back!”
Mikey reluctantly pulled back.
“Yeah, about that, Leo… I’m not coming back.”
Mikey what are you talking about “ 


So, Mikey can’t go back to the Footclan cause by this point Mikey had stopped Shredder from defeating Splinter (earlier drawing scene I’ve done) and if he goes back the Shredder will kill him.

And then this is where the turts hear the truth of what happened from Mikey and start to question their loyalties.

Anyway Its complicated, but it make sense in my head. Hopefully it does here too