Previously in The Citizen you had taken control of an important combine message relay, making the most of a failed mission to assassinate Dr Breen. It was located in a large conference building situated near a rebel safehouse - the Spare Time Cafe - from which your assault was originally launched.
The cafe was later raided by combine, and ultimately destroyed. No rebels were present at the time, but something there led the Combine to the Elvet Theatre - a more important rebel hideout. The attack on the Elvet was devastating, causing much of the rebel command structure to be seriously disrupted.
The second chapter of The Citizen picks up precisely where the first left off. You regain conciousness, and discover the extent of your injuries.
Mercifully, help is not far away. But then again, neither are the Combine.