What do I do after killing Garnier de Naplouse

There is no continue option in the Animus since the story itself is over. You just jump back to a location in the memories section and continue finding flags, etc.

The best place to jump to is Memory Block 6, since from there you will have access to all areas of the map. You could also jump directly into an earlier memory and you will still have all your unlocked abilities and gear, but parts of the map will be locked.

You had to pick-pocket Warren's pocket when he stands over by the window to get his pen to access his computer, then read his emails to get the password to the conference room computer. He stands over there a lot, but I missed it too, so don't feel bad.

If you're already at the end, and he's already left for the last time though, then I'm afraid that there's nothing that you can do short of just starting a new game on the main menu.