If Jennifer decided to kill Ellie instead as payback for her killing Charles. Jennifer would then take out the people in the helicopter but because she cant fly it. She uses her earpiece to request for a pilot to fly her to the government base Jennifer would then go to sacrifice herself to stop the n-bomb unlocking a new ending.
If Jennifer chose to forget about Ellie and stop the n-bomb. Ellie gets her best people to take down Jennifer instead of ramming them down in chapter five after getting her memories back. This would mean the n-bomb causes its explosion with Ellie and her survivors getting away with it.
So you all got the best ending you can get.
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I Forget the Way you Fight
FanficJennifer awaits to get her revenge on Ellie for taking away Charles from her.