Any theories as to what has been happening to the city.
 

As we have been focused on the North Hampton farm and not the city, what theories do people have about what is going on in the city?

My guess is the because of the invasion the government has been trying to stem a nation wide panic. So the only thing the Country knows is that something has happened but details are not being devulged at this time.

Donnie's mech fried the city's power grid and that brought things to a grinding halt for the Kraang. Enabling the EPH to go in round up the Kraang mutations, evacuate any innocent civilians they can find And/or quarantining the city so nothing gets in or out.

Donnie's Turtle mech has probably been picked up by the EPH along with some Kraang tech.
Shredder has taken over much of the Kraang technology for himself. The Kraang still exist but Kraang prime is no longer in power.

All mutants in the city are to be found and brought to him so he can determine their usefulness to him. He is also trying to learn where the Turtles and their friends are hiding so he can eliminate them.

Splinter has been wondering through the sewers looking for his family. He has found a new lair for them, and has risked moving his sons belongings to the new lair. Even if it's just for the hope of having something for them return to. He has hopes and prays that wherever they are they are safe and looking after each other. But each day that passes without contact weighs heavily on his shoulders.

I'm wondering if Splinter will have to team up with tanks like LH and Slash. Seems like every mutant in the city, including villains like Snakeweed and Spiderbites, has a common enemy in Shredder and The Kraang. Although if Shredder decides to pay some of them to hunt down Splinter, that could make things more interesting. I can't wait to see the return to New York stuff.

^
I really wonder how Slash is doing in all this.

Splinter, Karai, and co form a resistance movement, while Snakeweed and SpiderBytez try to catch them for the Kraang. Mutagen Man is found by the Foot and re-heated to serve as a soldier in their ranks.

I think Shredder assumes he killed Splinter but he wants proof of that. So maybe getting mutant soldiers by telling the less then savory characters who have been mutated to find the Turtles and Hamato Yoshi's body and deliver them to him. And he would reward him with the means to return human.