The only group in the Commonwealth willing to actually fight the Institute is the Railroad, an organization almost as secretive as the Institute itself.
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The Railroad is a secret network operating on the Eastern Seaboard in direct opposition to the Institute of the Commonwealth.
The origins of the organization are murky and lost to time, due to the numerous times the organization was nearly wiped out. The current incarnation has its roots in the remnants of the organization that persisted after an Institute raid that destroyed the faction's headquarters in November 2266. With thirteen survivors, Wyatt held an election and started to rebuild the organization from scratch. The first lesson learned was operational security - under Agamemnon, the Railroad was centralized and the Institute could - and did - easily learn where their headquarters were. The result was a single survivor, John D, and an organization in tatters, abandoned by most of its members. The new Railroad was constructed like a pyramid, in an effort to limit the information flow and prevent another HQ massacre. The first success came in February 2267, with the liberation of their first synth. Wyatt threw a party to celebrate, keeping to himself the knowledge that another runaway was recaptured by Coursers before they could get to them. However, the streak didn't last. Following the escape of an entire Institute work crew in March, the Institute wised up to the Railroad's continued existence. One safehouse fell in March. Then, in December, they located the Railroad HQ again and invaded it. Wyatt was gunned down, but many Railroad members managed to get out of the bloodbath thanks to Deacon. Pinky became the new leader of the Railroad, quickly implementing the lessons taught by the raid.
By 2275, the Railroad was back in business, focusing on moving rescued synths out of the Commonwealth. Despite his accomplishments, Deacon was kicked out of the HQ by Pinky for being, quite, a "lying, face-changing son of a bitch, unquote. Pinky continued implementing changes to the Railroad's operations, but they were too little, too late to address glaring issues. One of the crucial changes was the decision to remove all synths from the Commonwealth as soon as possible, following a homestead massacre by Coursers around January 2276. Around this time, Victoria Watts was also sent to the Capital Wasteland on the trail of Director Zimmer and his Courser bodyguard, Armitage. By September, the Railroad lost another safehouse due to Pinky's sloppiness. Desdemona's renewed campaign against the current leader eventually led him to stepping down.
The new leader took the position around December 2277. Desdemona narrowly won against Doc Carrington, immediately beginning work on improving the Railroad's security and success rate. With a 50-50 chance to recover synths, morale was a constant issue. To rectify Pinky's mistakes, the first step was improving operational security through reconnaissance, counter-intelligence, and stricter compartmentalization. Second was improved response time for synth recovery.
The first results started arriving in 2279. The Railroad grew and new techniques were implemented, including Railmarks and dead drop improvements. Out of a total of five synth escapees, two were recovered by the Institute, one was lost in the field, and two were saved by the railroad. However, this wasn't a lost year, as the HQ core team grew with the inclusion of Tinker Tom, a survivor of an Institute attack on a farm. Though disturbed, Tom would go on to become a key asset of the organization. A year later, Desdemona added Glory as a field agent and heavy. Tinker Tom grew increasingly eccentric under stress, but he was retained due to him being essential for maintaining the Railroad's gear and tech. 2280 ended on a relatively high note, with two escapees, no losses, and just one reclamation.
It was the quiet before the storm. The Institute hit the Railroad's HQ in full force in 2281, with lookouts managing to give only 30 seconds of warning. Fortunately, casualties were light. The biggest gain of the year was the discovery of the Switchboard, an old DIA facility with P.A.M. The predictive analysis machine impressed Desdemona enough to bring her on board as an essential part of their planning. P.A.M.'s initial reservations about aiding the Railroad changed after Glory interacted with the machine and soon, P.A.M. was an important component of Railroad operations. However, as if to compensate for this, The Institute compromised another safehouse, forcing the HQ to relocate with barely an hour to spare. That did not break the Railroad, however. P.A.M. continued to serve as a vital source of intelligence, though her predictions and proclivity for requesting odd data caused reservations among the HQ crew, with Deacon loudly arguing for shutting her down (and getting shut down in turn).
Perhaps the biggest breakthrough came in 2283, as the Railroad discovered that they had an ally on the inside. Codenamed Patriot, he first came to the fore after a synth escapee arrived in Diamond City with a map, instructions, and a coded holotape in tow. Intercepted by Old Man Stockton, she was the first of five synths. All with care packages and codes. This resulted in an expansion of their operations. By 2284, the coded holotapes were finally decoded by Tinker Tom, and were revealed to contain two words: Mass Fusion. The expansion of the Railroad's operations resulted in eight escapees with just one loss and one reclamation. The Railroad also began trying to discover the location of The Institute in earnest, but found it impossible to do for a variety of factors - the most important being that the organization has no records of its existence prior to 2266 and Wyatt assuming control. While the HQ was compromised again in 2285, the Railroad persisted. They relocated to Switchboard and continued rescuing synths, managing to save nine, with two lost to lynch mobs and one reclaimed by the Institute. The good streak persisted into 2286, with Institute sightings completely ceasing for three months. However, this was once again the calm before the storm.
The Railroad is constructed like a pyramid, with the base composed of informants and sympathizers (referred to as tourists), above which stand runners and safehouse owners, then an even smaller group of field agents, and finally, the most secretive and heavily protected headquarters crew that has access to all the information and coordinates Railroad operations.  As the organization practices strict compartmentalization of knowledge, information is issued on a need-to-know basis, with its members and cells operating in isolation from each other, following lessons learned in 2266.
As far as the Institute is concerned, androids are mere machines with no free will of their own that exist only to serve their creators. However, the Railroad stands by the doctrine that, even as machines, self-aware androids look, behave, think and feel as humans do, entitling them to the freedom intrinsically enjoyed by human beings as well as emancipation from their owners. The Railroad also occasionally assists human slaves when able, although they cite that there are many other abolitionist groups specifically focused on slaves, but no other group can aid with the unique challenges of concealing androids.
To this end, the Railroad employs the skills of computer science experts to alter the memories of the android to provide them with a clean slate, as well as the skills of a plastic surgeon to conceal the android's true identity. A Railroad branch in the Capital Wasteland recently aided an android (designation A3-21), but the operation was so risky that the branch had to temporarily shut down to keep its members safe until Commonwealth investigators abandoned the manhunt.
The Railroad is naturally opposed to The Institute and its practice of enslaving synthetic human beings. The Institute reciprocates this in any way it can, usually by attempting to wipe out the organization as much as possible. They attempt to keep a low profile and aid runaway synths by providing them with a new identity and aiding in their escape. In return, the Institute attempts to purge any safehouses it comes across and wipe out any Railroad agents, sympathizers, or informants they find. The Railroad is also opposed to the Brotherhood of Steel due to their ideology that synths are abominations and shouldn't be allowed to exist.
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The Railroad is inspired by and alludes to the Underground Railroad, an organization that dedicated itself to helping black American slaves escape their servitude during the 19th century.
The Railroad appears in both Fallout 3 and Fallout 4.
- ↑ Railroad HQ terminals: "2266 Nov
Gathered surviving runners, held an election. I lost, or won, depending on how you look at it. After the HQ massacre, most people simply left the Railroad. Only one person survived HQ, a runner named John D. He called out for volunteers to get some of the old files. No one stepped forward.
My job is to rebuild the Railroad from scratch. I think where Agamemnon went wrong, is that HQ was known by too many people. I'm theorizing here, but once the Institute hit a safehouse and leaned on anyone the HQ would be easy to find. But how could Agamemnon know just how deadly those damned Coursers are?
Current count: 13. 0 synths.
How the hell do we rebuild from here?"
- ↑ 2.0 2.1 Railroad HQ terminals: "2267 Feb
Got our first synth out of the Commonwealth last month. Threw one Hell of a party.
What people don't know is another runaway was recaptured by the Coursers before we even got to them.
John D has been finding tourists at a pretty good clip. But he keeps their identities to himself. Operational security he calls it. It makes me grind my teeth, but he's probably right. I think our whole organization needs to be more like a pyramid. A broad base of tourists that help out, mainly with information. Then the runners and safehouse owners in the middle. Then agents. Then HQ on top of that."
- ↑ Railroad HQ terminals: "2273 Mar
A whole work crew of synths escaped together. Five synths at once. We're scrambling to keep them hidden. Coursers have been spotted looking for them. They found one of our safehouses, but no one there knew where our HQ is. John developed a dead drop system we've been using.
Some vocal elements (Toby) say we should shut down. But that's a year and half worth of synths."
- ↑ Railroad HQ terminals: "2273 Dec
I just found Wyatt's journal. For whoever runs this outfit in the future, I figure you should know how we messed up.
We were running the Workgroup Five out of the CW when Coursers found our HQ. Total shitstorm. Deacon (that's what he's calling himself now) had an escape route planned, and most of the survivors owe him their life. Wyatt didn't make it past the first hail of bullets.
Something everyone should know: if one safehouse goes down assume that all Hell's coming for your ass, because it probably is. Always, always, ALWAYS assume the Institute has resources beyond what we can imagine.
From now on only the heavies leave HQ. And we got to move our packages fast. This slow crap hurts more than it helps."
- ↑ Railroad HQ terminals: "2275 Jun
Damn it. We got two synths, or packages as we're calling them now, out of the CW. Running the 3rd and a Raider gang caught them. Total blood bath.
P.K. almost lost his package near Danvers, too. I kicked Deacon out of HQ, got sick of the lying, face-changing son of a bitch. That month he spent as a Ghoul freaked a lot of people out.
Going to keep running hard."
- ↑ Railroad HQ terminals: "2276 Jan
Lesson: move all packages outside the Commonwealth.
Lamda 8 homesteaded off Parsons. She got married to a farmer. Coursers found her and it got bloody. Lost Lamda 8. Her wife almost bit the bucket, too.
Courser spotted heading south (with company). Watts volunteered to track them."
- ↑ Railroad HQ terminals: "2276 Sep
Desdemona is a real pain in the ass. Keeps harping on every little damned thing. Worse than Deacon and Carrington combined.
We lost a safehouse and went to ground. SOP. Desdemona says I'm being sloppy. I'm getting sick and tired of leading these misfits."
- ↑ Railroad HQ terminals: "2277 Dec
After we lost Trinity, Pinky Thompson stepped down. It took some persuasion. We held a vote on who should run the Railroad. It came down to me and Carrington. Might be a problem there.
The doctor, Deacon, and I have been analyzing the many, many mistakes of Pinky. Our "batting average" is roughly 50/50. Only a few synths a year make it out. It's hard to keep motivated when failure is so epidemic.
We're going to hit the fundamentals: operational security. Look outs, counter-intelligence, and compartmentalization. We need to reduce the response time to find a new synth runner."
- ↑ Railroad HQ terminals: "2279
2 escapees. 1 loss. 2 reclaimed before interception.
Added a new member to core HQ. Thomas Weatherby. An Institute grenade did a number on his family farm. He's rattled but very, very smart. Hoping he can arm us with something better than pipe pistols.
Organization grown. Devised rail signs and improvements to dead drops. No Coursers spotted all year. Merry Christmas."
- ↑ Railroad HQ terminals: "2280
One of our rescues, G7-81, took a strange turn. Most synths are traumatized and go through the procedure with Doc A. G7 opted out. Begged to join. Did some crazy stunts with High Rise at Ticon.
Called her into the HQ. Promoted "Glory" to heavy. She's well suited for the role (perhaps too much so).
Been working with Tom. Brilliant, but he's getting increasingly eccentric. Carrington says the stress is causing severe psychological problems. But he's too damned essential. God help me, I'm keeping him on.
2 escapes. No losses. 1 reclaimed. Quiet year. Less chrome domes in the field than the last two years. No idea why."
- ↑ Railroad HQ terminals: "2281
Where to begin?
Year started like shit. Coursers came out of nowhere. They found the Farm, lookouts only gave us 30 seconds of warning. Torched what we could, casualties light.
Relocated to the Beast. Then one of the B team scouts, Tommy Whispers, made the find of the century. An old DIA facility, "Switchboard." Called him up to HQ (overdue), Glory's taken him under his wing (God help him). Tom relocated to the Switchboard or Facility X as he calls it. Then he sent an urgent message.
My first meeting with P.A.M... Can't describe. She made some predictions, frighteningly accurate. Asked for data. Started feeding it to her. Very reluctant to help the cause. But after a long talk with Glory she's on board. No one knows what Glory said to PAM. Deacon jokes that PAM has a crush on Glory. Certainly PAM acts different when she's around. But there's nothing emotional about PAM.
With PAM's prediction managed to anticipate a run-away.
Year ended badly. We had a synth infiltrator at Mercer. Deacon caught her before P.A.M. But damage done. Blew the Beast and moved to Bolthole. Only an hour to spare before the Coursers came.
2 escapees, 1 loss, 0 reclaims."
- ↑ Railroad HQ terminals: "2282
Promoted Tommy to be our second heavy. Tom made him a custom pistol, the kid's frightening with it. P.A.M. has us running strange ops for data. She's not always right, but right enough to be a trap. Too tempting to rely on her predictions. One day Deacon recommended moth-balling her. Took an hour to talk him down.
2 escapees. Not many runners this year."
- ↑ Railroad HQ terminals: "2283
One word: PATRIOT.
Our second package of the year was different from the start. Didn't behave lost. Ran in a straight line to Diamond City. Old Man Stockton caught her before she caused too many waves. She wasn't supposed to be on the work detail and had a care package: a map, instructions, and a coded holotape. Tom's been useless all year trying to decode the damned thing.
Third package went straight to Diamond City again. Set up Old Man Stockton as the gatekeeper. Then a fourth came in after a week. All with care packages. All with more codes. Someone on the inside is helping us. Code-name PATRIOT.
All told 5 escapees this year."
- ↑ Railroad HQ terminals: "2284
An incredible year. Everything's coming together. Tom broke PATRIOT's code, said it was designed to be broken (whatever that means). Just two words, "Mass Fusion." Sent some recon there and found nothing. Found out later why.
PAM's been trying to find the location of the Institute in earnest. Failing. Deacon's convinced the solution lies in the past, not future. Deacon already knows the big secret - we know nothing about the Railroad before Wyatt was in charge (or is Deacon Johnny D???).
Deacon's been digging into Institute sightings from years, even decades before. Or at least, that's what he says. Getting really tired of all his lies.
Coursers caught Package 7. Almost nailed Old Man Stockton, too. One of our scouts found Package 8 heading to Mass Fusion. The coded message he carried was another location, Prospect Hill.
8 escapees this year, 1 loss, 1 reclaimed."
- ↑ Railroad HQ terminals: "2285
Busy. We're in Switchboard now. Bolthole went down on fire. Coursers getting very active. But, by God, we're rescuing synths. 9-2-1. Both of those 2 were from goddamned lynch mobs."
- ↑ Railroad HQ terminals: "2286
A dry year. Coursers, work crews, and synths vanished for three months. No idea why. Worked on fortifying Switchboard. Deacon was barely here all year. Chasing ghosts.
- ↑ Deacon: “So I'll be straight with you, although you're not going to like it. I have no idea what the prototype does. Us Railroad agents are treated like mushrooms: kept in the dark and fed... well, you get the idea. It's got to be important, though, Dez wouldn't risk our hides lightly.
- ↑ The Lone Wanderer: "Sounds like slavery to me. You sure they don't "wander off" on purpose?"
Zimmer: "Nonsense! This is a machine we're talking about. Can you enslave a generator, or a water purifier? Of course not. The same principle applies. But let's get back to your mission. You are to find this missing android. I've tracked him to somewhere here in the Capital Wasteland. He must have done something drastic, like facial surgery and a mind wipe, or else I would have found him by now. It will be no easy task. He may not even realize he's an android. Don't upset him by talking with him. Just come get me immediately. I'll handle it."
- ↑ 19.0 19.1 The Lone Wanderer: "What do you know about this android Railroad?"
Horace Pinkerton: "Bunch of bleeding heart morons if you ask me. They're going to get themselves killed one of these days. And for what? Machine liberation? But, they have brought me some really interesting tech over the years, so I guess they're okay. And that android! He was the chance of a lifetime."
(Horace Pinkerton's dialogue)
- ↑ The Lone Wanderer: "Anything else I should know?"
Victoria Watts: "Just understand that this android is now, for all intents and purposes, a man. He looks human, he acts human. He believes he IS human. But even if he's not... Even if he's a machine... He's capable of rational thought. And emotion. So you see, his soul is as human as yours or mine. This person -- and he is a person -- deserves a chance at freedom. Please, if there's a shred of decency in you, don't take that away from him."
(Victoria Watts' dialogue)
- ↑ The Lone Wanderer: "What about human slaves? Don't you try to help them, too?"
Victoria Watts: "Yes, if we are able. But there are others in the Wasteland who assist in the plight of human slaves. Our android brethren have only us."
(Victoria Watts' dialogue)
- ↑ The Lone Wanderer: "I know you're part of the Railroad. What do you know about the android?"
Manya Vargas: "A while back they were asking around for a computer genius to give our friend a new set of memories. You know, a clean slate and all that. Pinkerton at Rivet City took care of him a while back. Was a complete success. No one will recognize that robot now. I'm glad. But you hush yourself about all that. The hounds are still out sniffing around."
(Manya Vargas' dialogue)
- ↑ The Replicated Man
- ↑ The Lone Wanderer: "I know you're part of the Railroad. What do you know about the android?"
Tulip: "They were looking for a tech wizard a while back. Someone who could fiddle with the android's memories. But you better stop poking around. Those Commonwealth hunters are still out there, tracking him down. We shut down the Railroad for safety."
- ↑ The Lone Wanderer: "I'm interested in this android from the Commonwealth."
Herbert Dashwood: "We don't do that anymore. Well, not until the heat dies down. For now, the Railroad is shut down. Used to help them escape from the Commonwealth. Find them places to lay low. The last one was someone real important. They are still looking for him."
(Herbert Dashwood's dialogue)
- ↑ Railroad HQ terminals