So this is how Mikey escapes into the world that Donatello has been steadily murdering over the past year.
But they are both still chipped, so it's not like Donatello won't eventually find them.
However, Donatello is currently dealing with Raph in his turtle experience so he's distracted, and then he has a whole year or so to retrain Raph into Raphael. 
Mikey and April might put some decent mileage between them and New York in a year, but I'm pretty sure those chips can be found via Bishop's satellites.
Still I know there is more to come.  Like you torturing Leo for several chapters for our amusement before his untimely demise at Raph's hands.

Will we eventually get a final story?  The "What Comes After," it's all said and done with Leo's pov?