Once you beat the game (after you see the credits,which you cannot skip.) wait for the credits to end and wait for the doctor and Lucy to leave the animus room. HIGHLY RECOMMENDED BUT NOT REQUIRED: walk around the animus room and your bedroom using eagle vision(yeah you can use it now!)and try to solve the puzzle,you read it from the bottom right to top left, I'm not sure what it says so don't ask... After they have left, walk to the animus table (the side where you normally lay) and the "press any button to continue" message will appear....so press any button. Your character will lay down and then you will see the animus menu, you know what to do from there :).
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You get in during the credits.
SPOILER ALERT
there is a another pessimal piece of combat as Desmond and everybody. The screen goes black as credits start rolling after the combat and you hop into a vehicle with them and all of the tools. you get back onto the animus inside the vehicle as you head north. you simply start playing as any other open-world game. doing missions, finding feathers. etc.
You can't leave the Animus manually in Assassin's Creed 2, but you will be pulled out of it at set intervals as the story progresses.