Raph had died... He saved Leo's life but Leo still lost his hand. His stump is still in bandages and it still hurts him.

You get into the med bay and see Leo sitting on the bed, Mickey holding the one hand Leo has left and Donnie... Donnie was just there he was sitting in the corner, his eyes out of focus.

"He's gone... Dead...?" Leo was still in shock. Mickey just squeezed Leo's hand tighter rubbing it with his thumb. Donnie was still quiet.