After Splinter's death & the defeat of Shredder Leo, Raph & Donnie go their separate ways for varying reasons, each believing they were the only one leaving but a lack of communication means Mikey is left home alone.
They had just escaped the city by hiding out at April's old farm house. Considering everything they all have lost, everyone is miserable. And Mikey? Well...he's struggling with SH, but someone helps him realize that things won't always be miserable.