Fully research the Houdini Splicer. Have Natural Camouflage equipped.
Immediately before the final battle, remain idle, and you will become
invisible. No one will attack as long as you do not move. If you move,
you will become visible again, and all enemies will attack; you cannot
turn invisible while being hit. Once Eleanor says she can fight, summon
her. She will distract and fight everyone, allowing you to stay
invisible. She will eventually kill everyone so that you can escape.