1) The Governor and Aubrey hook up and all is cute and rainbows :3
2) The relationship progresses and Woodbury expands happily with Aubrey and Merle staying at the town :3
3) Machonne and Andrea show up at Woodbury and things proceed as they do in canon except The Governor sends his men after Machonne with the offer to accept her back. She refuses and the fight happens as it does in the show :3
4) Merle finds Glenn and Maggie and kidnaps them when it is revealed to him that Daryl is alive :3
5) The torture scene goes a bit differently. In this one though The Governor focuses entirely on Glenn. When torture doesn't work he puts Maggie in another room and secretly has some of his guards go into the next room and make it sound like they're viciously beating her before they rape her. Glenn gives in and tells them. Maggie is brought back into the room unharmed, letting Glenn know it was a trick :O
6) Merle and the scouts go to the prison to scout it out on The Governor's orders ^^
7) The rescue team arrives for Maggie and Glenn! The Governor tells Merle that he wants to recruit the stronger members of Rick's group for Woodbury but leave behind some of the dead weight or rebellious ones (Carol and Michonne here)
Michonne waits at The Governor's home and kills Penny like before. The Governor loses his eye but Aubrey manages to get inside and scare Michonne away
9) The Walker fight does not include Merle this time so it's just Daryl fighting of several Walkers without any weapons. Aubrey says it's cruel but The Governor says it's the will of the people. Merle is conflicted as to who he wants to help out