I do not own anything involving Fallout. (Thank God Cause Fallout 76 suckssssss) Just to let you all know (there's not much of you out there) but I'm basing this story off of my play through of Fallout 3 and 4. Now in Fallout 4 there is a way to take out the Institute without having to kill of the railroad or the brotherhood. This is not a glitch or anything. You just have to play along in the game until you get a quest from the brotherhood (I think it's the one where you go to the island where all the super mutants are at) you get that mission but never go to it. You then switch and complete all the minute men missions. At the end every other faction will be happy with you and you'll be in good relations with them.
Sorry I am trying to world build so this story is a little light on the action and heavy on the talking.
Declaration
Dr. Li took off her glasses and rubbed her temples. "Where do I begin?"
"How about the truth." The Wanderer snapped at Dr. Li.
"Its not that simple." Dr. Li began. "Your father was raised by one of the most secretive groups in the world. For a very long time, most people didn't even believe the Institute was real. That is the level of secrecy this agency lived under."
"So our entire lives, Dad lied to us?" Amanda stated coldly.
"Yes, and no. He is a product of his upbringing. The Institute, puts or put its secrecy above everything. They took secrecy so seriously that when people did get to close to the truth, they tended to disappear."
"So they killed people?" The Wanderer stated, "I'm telling you Doc, this Institute isn't sounding like they are angels here."
"No, I guess they don't. But, you have to understand what the Institute's end goal was. Everything they did really was for the betterment of mankind. They wanted to bring the world back from this wasteland."
"Wait," Amanda interrupted, "I'm still confused about Dad being born before the bombs dropped. How is that possible, he would be like 220 years old. Was Dad some kind of smooth skinned ghoul or something?"
"No." Dr. Li said, "Now, I am being honest here, I don't know everything. But your Dad told me that he was born about 4 months before the bombs fell. On the day the bombs fell, he and his family went into Vault 111, and then they were cryogenically frozen. The Institute eventually went into the vault and retrieved your father."
"Wait, so is the Institute like part of Vault Tech?" The Wanderer asked.
"God, no." Dr. Li stated with a shake of her head. "Now Vault Tech, that's an evil company. The more we find out about them, the more questions are raised."
"Sorry, Dr. Li, but I don't give a damn about Vault Tech," Amanda said, "I want to know about my father. Why did this Institute take our dad, from the Vault? How did they know about him." Amanda then jumped out of her chair, "Dante, our grandparents may still be alive."
The Lone Wanderer stood up as well, "You're right, we have to get to Boston."
"Wait, wait," Dr. Li said waving her hand trying to get the two siblings under control. "James told me that there was a malfunction in the cryo-pods, and that only the pod he and his mother was in was working. Everyone died in that Vault."
"Wait, so our grandmother is alive?" The Lone Wanderer asked.
"No, Shaun or James," Dr. Li shook her head, "Your dad, won't talk about it, but he did say she died soon after the Institute Opened their pod."
"So, why did the Institute, take Dad? From everything you're telling me I don't think it was to save him." The Lone Wanderer stated.
"It was, in away. The Institute was started when the bombs fell. A group of scientist in Boston was able to get to safety on that day, and they began to build what became the Institute." Dr. Li sat back down. "Like I said the Institute's goad is to make the world to what it was before the Great War. That's why they began to build Synths. A Synth for the most part is immune to radiation, and can go places humans can't. "
"Ok, but that's still doesn't explain why they needed Dad?" Amanda said.
"It does. You guys have seen A3-21."
"For the very last time, Doctor. His Name is Harkness." Dante said coldly.
Dr. Li nodded her head, "I'm sorry Harkness." Taking a deep breath Dr. Li continued, "Please what I'm about to say, in no way is intended to disrespect Harkness in anyway." She looked at the Lone Wanderer and then at Amanda. Both of them nodded their heads, "Harkness in almost all ways can pass as human.
"He is human." Amanda interjected.
"Maybe to you," Dr. Li held up her hands to forestall the outburst. "Harkness is a synthetic creation. His A.I is so advanced that yes, he can feel and think just like you and me. Hell there are some synths that can even reproduce like humans can. And that, that is because of your father."
"So, Dad invented them that still doesn't explain how the Institute knew he would be that smart when he was just a frozen baby." The Lone Wanderer stated, getting visibly irritated.
"I'm getting to that. And no he didn't invent the synths. In the beginning the Institute was able to develop the A.I to the level they are at today. However, what they couldn't do is create the realistic body that the synths today have." Dr. Li, leaned back on her chair, and rubbed her head. "The bodies that what we call generation 3 synths, are made from real human cells. From what I have been told every attempt to create a synthetic human body was met with failure, due to the fact that every human in the world to include those living in the Institute have some level of radiation poisoning in them. Everyone, accept for those living in a vault."
Dr. Li continued, "Now the Institute new of several vaults that still had people who lived in them that were not exposed to the radiation, but even they were demeaned to be inferior."
"Why's that?" Amanda questioned.
"Well, you two would know. Think about Vault 101, the vault you two grew up in. All of the people there with the acceptation of you two, are descendants from the original vault dwellers. Well after a few hundred years, the chances that most of if not all of the people there would have had some type of inbreeding is extremely high. This would make any genetic sample taken from one of these vault dwellers to be less than ideal. But when the Institute discovered a vault who had humans that were alive from the time of the war, and that their genetic structure would be pure. Well, that was something they couldn't pass up. And because of that, the Institute found your father, and using his DNA, they were finally able to create, a truly real synthetic body. It's so real that only a deep, detailed body scan, can tell the difference from a born human, and a synth."
The Lone Wanderer, starred at Dr. Li for a long time, "With everything you just told me, it just proves that me protecting Harkness, and all synths is right. In a roundabout way they are all my family."
"In a very loose way." Dr. Li said, "These synths don't share DNA with you. The Institute just used the genic code that they got from your dad, along with his pure blood to help create the bodies."
"Again, Dr. Li, I really don't give a damn, about all this." Amanda said irritably. "So, Dad was rescued by this Institute and raise by them. That doesn't explain how he got here. Did you forget doctor, I lived with Mom and Dad in Boston. We had a house and everything right in Diamond City."
Dr. Li smiled, "Yes, I remember. Those were good times." Looking at Amanda, Dr. Li nodded, "Again, I don't know everything. Even when your father took over the Institute, he continued to be very secretive. From what I gather, your father rebelled against those that raised him for a time. It appears your father got tired of waiting for change to happen and left to be that change."
"It appears he left the Institute, and that is when he met up with your mother and the group we worked with." Dr. Li smiled remembering. "When your father first met us, he was a breath of fresh air. He had knowledge of things that helped jump our research years ahead of what it was. He was so brilliant."
"And you never wondered where he came from." The Lone Wanderer asked.
"Oh, we wondered. We even guessed he was from that he was from the Institute." Dr. Li shook her head, "But we didn't really believe in the Institute was real. In the end he told us he was from Vault 81."
Vault 81?" The Wanderer questioned.
"Oh, sorry," Dr. Li said, "Vault 81 is much like how Vault 101 is now. They are the descendants of the original vault dwellers. And like Vault 101 they have opened their Vault to do some limited training with the Common Wealth."
"Please," Amanda practically shouted, "Don't get side tracked."
"Yes, of course." Dr. Li cleared her throat. "But well there's nothing really more to tell that you two don't know in some ways. With your father's help we was able to get Project Purity started. Of course now we know that with the Institute knowledge of the land, your father knew to come down to the Capital Wasteland to try to see if we could get Project Purity to work. And well, like I said you guys know the rest."
The room became silent. "So, James or Shaun, I'm sorry." Amata said, "He almost died trying to get Project Purity off the ground. He went back to the Institute became its leader. Do I have everything so far?"
Dr. Li nodded. "Ok, so I have some questions myself." Amata said. "First and foremost, why the hell did you come back to the Capital Wasteland with those monsters that killed people that were my friends?"
"I already…."
"I am not done." Amata stated, starring daggers at Dr. Li. "I gave you all the chance in the world to talk, and talk you did. And I did not hear anything that comes close to an explanation on why all those people at Rivet City died, or the damage caused to Springvale, MY HOME! Or putting Dante, MY HUSBAND in danger!" Amata finished, her eyes burning with rage. "You, Dr. Li better have a damn good reason, because if you don't." Amata shook her head.
"And what is your second question?" Dr. Li stated coolly.
"Oh, you bitch," Amata moved towards Dr. Li but was stopped by the Lone Wanderer. "I'm calm, I'm calm." Amata, breathed. "My second question is what happened to the Institute? And who killed James, Shaun, ahh whoever he was!"
The Lone Wanderer turned to Dr. Li, "She has a point, doctor. People died because of your actions and your people. You better explain and fast, because understand one thing I am not my father, I don't betray or abandon those close to me."
"Yes, well." Dr. Li began to slowly press a small button on her wrist, and then froze when nothing happened.
"Wondering what's going on?" Amanda said with a lifted eyebrow. "Now I won't pretended to understand what teleportation, but teleportation is not unknown to us. There is a shield around Springvale that prevents anyone from teleporting in or out of it.
"What are you talking about?" Dr. Li said coldly.
"Oh, you wouldn't know would you," The Wanderer said, as he leaned up against a wall. "You left a little after the incident occurred." The Lone Wanderer removed Ant's Sting from its sheath and started cleaning his finger nails.
"Dante, I was there at your birth, I help raise you for a time, I helped get you and your sister into the Vault." Dr. Li began to panic.
"I know, and that is why you are still alive." The Lone Wanderer stated.
"Where did you get teleportation technology?" Dr. Li demanded.
"Zeta," Is all the Lone Wanderer said.
"Zeta, what the hell is that?"
"You don't need to know." Amata stated, "You still have much to explain, and I suggest you make it good."
Dr. Li looked around the room and then sighed in defeat. "There really isn't much to tell. You would have never seen me again if it wasn't for that damn Sole Survivor."
"And who is he?" The Lone Wanderer asked.
"Honestly, I don't know. Like I said your father was very secretive." Dr. Li looked at the Lone Wanderer. "What I'm about to say is, partly based off of the information your father gave to the Institute staff and part guess work." Dr. Li stood up and started walking around the room. "About a year ago, the Institute started getting word of this Sole Survivor in the Common Wealth. From what we heard he was a force of nature. Kind of like you." Dr. Li pointed at the Lone Wanderer. "I actually believe this man was some kind of vault dweller, hell he might have been someone from Vault 111."
"This man, this Sole Survivor mowed down raiders, slavers people called him the Hero of the Common Wealth. He took out anyone that got in his way. He had training and tactics that most people didn't have, that they still don't have to this day. If I hadn't seen him myself, I would have thought he was a myth. This man rebuilt settlements and trade routes. And then, he took out one of our operatives. A very dangerous man named Kellogg."
"We started to panic, he was interfering in Institute missions, getting dangerously close to uncovering us. Because of him the Common Wealth was looking at the Institute as an actual faction and not just some myth. But Shaun just said, let him go. He said this man was going to take over the Institute when he passed." Dr. Li sat back down and shook her head.
"And then the day came. He somehow made his own teleporter and came to the Institute himself. We were told to allow him to come in. Your father welcomed this man in, offered him the keys to the kingdom and what did this man do? He spit in your father's face. United the Minute Men, The Brotherhood, and that rag tag group the Railroad together. He infiltrated our base and destroyed it all. This man set of a damn nuke destroying everything we worked for."
"How did you escape?" Amanda asked.
Dr. Li just looked at the floor. "How did you escape?" Amanda asked again.
"He gave us time. Alright. He came on the radio he told us we had to get out that he was setting off the nuke, a lot of us escaped."
"So, how did he kill Dad?" The Lone Wanderer asked, "Right now I can't say I'm sorry to see this Institute go."
"Haven't you been listening? Your father was dying. For the most part he was bed redden. He couldn't get out of bed, he couldn't escape. When that nuke went off your father, my friend was in the Institute. That asshole killed your dad, he killed him." Turning to look at Amata, "So, to answer your question, I came back to the Capital Wasteland with those coursers, to get back all those runaway synths. I didn't want anyone to die. But I am going to get every last one of those synths that escaped, I'll reprogram them and then I'll bring hell to this Sole Survivor. I'll turn his world to ash. I'll hunt him down, I'll make him pay for taking him from me."
"Who?" Amanda asked.
"James, Shaun whatever you want to call him. He was a brilliant man, he could have done so much for this planet, and I loved him." Dr. Li began to cry. "He chose your mother, and I was fine with that. But I got to be near him that was enough, but this, this Sole Survivor took him from me, and now, now I'll take everything from him.
Dr. Li continued to cry, as the Lone Wanderer stood there quietly. After some time Dr. Li began to calm down, "I'm sorry," Dr. Li said quietly, "I honestly didn't mean for the coursers to kill anyone. But they are soldiers, their programing doesn't."
The Lone Wanderer raised his hand to quiet her. "The Capitol Wasteland is under my protection doctor. Its people human, synth, or anything else is under my protection. You and your coursers are no longer aloud anywhere in the area." He walked over to Dr. Li and made her look at him. "Please, understand I see a courser, I kill that courser."
"Your father.."
"You don't need an army, Dr. Li. I don't think I could have ever supported the Institute or their methods. Hell if I had been in Boston I probably have done everything this Sole Survivor did."
"So, you're going to just allow your father's killer to go unpunished?" Dr. Li shouted at him.
"No." The Lone Wanderer said as he turned to the door. "I agree with what this man did, but he killed my father, he killed my family." The Lone Wanderer jaw clenched in anger. "You, don't need an army doctor, because I'm going to Boston and I'll bring Hell with me."