Splinter was missing and probably dead, Karai mutated and nowhere to be found, the lair was destroyed by the Kraang and was no longer safe, the Kraang invaded the city and kidnapped nearly anyone and took them to Dimension X, and Leo was beaten the crap out off him and left in a coma. That's how they left the city 5 months ago.
They found Splinter and managed to get him back to his own mind, Karai still missing, the lair guarded by Kraangs, Leo was better, and they found an abandoned Antonio's to live in for the meantime.
Donnie built a makeshift lab on the back to try and make retromutagen for Karai, it wasn't much, but it was helpful in the meantime. Leo and Raph were preparing to go out and back to the sewers to retrieve some of their belongings, as well as food, water, medicines and gear.
"You have your backpack ready? Remember to pack as little as possible so we can retrieve more." Leo tied his bandana back to his face. "Last time, we barely escaped with a few cases of food."