Just know that this is a fan creation that is based off of the Institute ending in Fallout 4.
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As Nate led Nick and Ellie up to the meeting room of the Institute, he had two armed.... humanoids in X-01 Power Armor accompanying him. Perhaps as bodyguards in case Nick or Ellie decided to fire on him? Or perhaps as an intimidation factor. Nick looked over at Ellie, who was clearly concerned that her and Nick had been taken to the main lair of the beast.
"Alright, we're here. The meeting room."
"Okay, so why are we here again?" Asked Nick.
"Because I'm here to discuss something with you and Ellie, of course. Now, please take a seat."
Nick and Ellie sat down as far from Nate as they could, as Nate sat down at the other end of the table from the entrance to the room.
"So, we are here to discuss how The Institute is now the primary authority in the commonwealth. And how we need more eyes in the street."
"I'm sorry, do you mean to tell me that you want me to work for you? The organization that I've been trying to find and been working against for years now? You think I'll agree to that?!" Stated Nick.
"Oh no, not willingly. You'll be installed with surveillance technology so that we can always see what you see and hear what you hear."
"And you think I'll let you do that?!" Nick said as he pulled out his Pipe Pistol.
"Once again, not willingly. Your memory of this day will be wiped and replaced with the memory of another boring day in the office."
"And what about Ellie?! She'll remember everything." Nick stated the obvious.
"Exactly why she'll be replaced. With a generation 3 synth. The synth itself has already been built."
"Then you truly have become the evil of the commonwealth."
Nick pulled the trigger of the Pipe Pistol, aiming for the head at his once friend, but the bullet did practically nothing to Nate, for as soon as the trigger was pulled, Nate's white and green lab coat had been replaced by combat helmet and a clean grey suit.
"I'm sorry Nick, but you do not fire on the leader of the Institute without consequences."
"Ellie, RUN!" Nick shouted.
As Ellie got up from her seat and ran to the door, she heard gun shots and then a loud noise behind her, meaning that Nick had surely been captured by Nate or the synths in Power Armor in the meeting room.
Ellie saw tube-like walkways to her left and right, and ran to the right, and saw there was an elevator in the center of the building.
Ellie ran down the stairs as soon as she could, but when she reached the elevator, the button did not work at all.
"Ellie, please calm down."
Ellie turned around, and saw Nate, with two X-01 Power Armor suits on either side of him, one of them carrying Nick, who seemed to be powered down somehow.
"We will not kill you if we replace you with a Synth. We can add you to the people here."
"That's- That's a lie! It has to be!"
"X6-88, grab her."
The Power Armored Synth that was not holding onto Nick Valentine approached Ellie, and before she could even attempt to avoid it, the courser had grabbed onto her arm, and took her away to the director's office in the Institute, with Nate following behind with a silenced pistol in hand.
When Nate and The Synth's left his room, Ellie was nowhere to be seen, so it was safe to assume that it had indeed been a lie when he said she could join the Institute.
Soon, Nick was brought to the Robotics division, with a new modification made to him to record everything he saw and heard all day, along with a memory wipe of the events of today.
Afterwards, the new Ellie synth was sent to the Valentine Detective Agency with the memories of Ellie given to it as to make sure it's cover was not blown.
Finally, plans to expose and rebellion formed could be counted as a success.
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Chapter 1 of the story has been completed. Nate's plans have begun.