Quite a but has happened.
Since the first Prison break, most people went with Tim and Dave to their base underground. Others stuck around, or near it. Some bad guys were set up and shit. Second Prison break happens. Introduces more characters. Some devastation occurs. More character and story development. Biggest possible villain is introduced (Jack Noir).
Everyone returns. People do their own thing, while others just disappear. The villains move in, and some fighting occurs, nothing too serious. Jack attacks and destroys everything. The Outcasts flee as Jack obliterates their home.
That's where we are now.