Fully research the Houdini Splicer. Have Natural Camouflage equipped. Just before the final battle, remain idle and you will become invisible. No one will attack. Do not move or you will become visible again, everything will attack, and you cannot turn invisible while being hit. Eventually Eleanor will say she can fight. Immediately summon her. She will distract and fight everyone, allowing you to turn invisible. She will eventually kill everyone so that you can escape.