Get used to Mieville leaving a lot of things open, he's not an author that feels he has to leave this all wrapped up neat and tidy.
Iron Council is actually the third book dealing with the City of New Crobuzon. The second book, The Scar is set just after Perdido Street Station, but doesn't really feature any of the main characters from Perdido Street Station. The main character is a former lover of Issac's who decides it might be a good idea to get out of the city for awhile in the aftermath, and finds herself caught up in an adventure involving pirates, a large floating city made out of boats and adventure, of course. The Scar is good, but not as great as Perdido Street Station.
Iron Council is set many years after Perdido Street Station and the city is being torn apart, both within and without. War with Tesh is looming, and rebellion and rioting is loose in the city. A small group of renegades sets out to find the Iron Council, a lost legend, A group of rail workers who rebelled, and stole a train and the train tracks and headed off to run their own communist style community. It's a nice idea, of this group going where they want by constantly ripping up the tracks behind them and laying them in front of the train. The rebels want the Iron Council to return and set New Crobuzon to right. Mieville gets very political with this one and in my opinion, of the three novels Iron Council is the weakest.