Basically, this is what happens in the comics and most of which, will be adapted into season 3/4
They arrive at the prison, clear the outside, open the main door, begin to clear the inside, the riot room, cells etc... then they get to the canteen, it's locked and seemingly no way in, they eventually pry the door open (this is where one of the comics ends)
The next comic starts with them opening the door to find......4 prisoners sat eating in the canteen as if no zombies even existed.
They talk with the prisoners who explain that when the prison became infected they were all working in the prison canteen, they had plenty of food (considering its a prison they would have had enough to feed the entire prison for a while) so they thought it best to lock themselves in there, since it's fairly secure, and just left the guards and rest of the prisoners to die.
They agree to help Rick & Co empty out the rest of the prison so they can all live there safely and securely (obviously since this is The Walking Dead that doesn't happen).
On a routine scouting trip for food, they see the helicopter (shown at the end of season 2) but the helicopter crashes, Rick, Glen and a few others decide to go and investigate, find the helicopter, but no bodies, they (probably with the help of Daryl in the TV show) track the foot prints to a town called Woodbury (this is where the Governor comes in, he runs Woodbury, keeps the residents safe etc..
Rick meets the Governor and attempts to build relations (and fails) turns out the Governor is bat crap crazy and makes Michonne find a guy in a brutal death match surrounded by walkers. Michonne, being the bad ass that she is, kills some dude and the walkers, finishing the brutal game.
The Governor, displeased with this, takes Michonne prisoner and repeatedly rapes her (interested how they're going to do this on TV) Michonne escapes and cuts the Gov to shreds, but he lives.
Rick & Co escape Woodbury with the help of someone (who later turns on them) and go back to warn everyone else about the Gov and Woodbury)..