Lori and T-Dog's deaths were fakes and they are hiding in the prison, because they hooked up and didn't want anyone to know about it. Lori loaded Carl's gun with blanks.
No one died this season, not even Merle. We flashback and see that Daryl killed some other zombie with a prosthetic arm that he imagined was Merle.
There were no living prisoners, either. They found 5 corpses in the cafeteria and Beth wrote stories about them interacting with Rick's group (turns out she's been chronicling events and what we've seen is her fictionalized account of the survivors' struggles).
Then Bobby Ewing steps out of the shower and discovers that JR is a zombie and Superman 3 and 4 never happened.