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.