I don't entirely remember this to be honest, but once you kill the last guy and finish the game off, if you sit through the credits you can then go back to any of the memory blocks and collect flags or kill templars or whatever and it will autosave and then you're free to do what you want.

I watched the credits and i wanted to go back and get flags but i wasnt able to everytime i loaded the game it would go back to reality like when you finished a memory block and i couldnt do anything but go in my room and hit y

yes that's it. you hit y and then the crepits appear. you have to watch the credits all the way through, then you will appear back in reality again and you can then use the animus and go where you want. Make sure you collect a flag or kill a templar at this point though so that it definately saves, otherwise you will end up having to watch the long credits again.

www.gamefaqs.com/boards/genmessage.php?board=930278&topic=50268844

Unfortunately, there's no known solution short of starting a new game. Sorry.