Curate, connect, and discover
*a vague conspiracy theory which doesn’t actually answer the question at hand. We all have our own ideas of how the lore should go, and I’m sure yours is very canon-compliant and valid, but this is mine and I have support for it. Looooongpost.
First off: What do we know about the canon Wanderer?
We know they activated Project Purity (or had a companion do it) without the FEV and were inducted into the Brotherhood. We know they’ve met with MacCready (you can’t finish the game if you don’t), and he has dialogue indicating they had further contact. They also took the Brotherhood’s side at Adams Air Force Base.
We don’t know what happened with The Replicated Man, but since the canon Wanderer appears to have good karma, and info from 4 implies Zimmer’s disappearance was more recent than ten years ago, it seems likely they took the boring ending, which secures their membership in the Railroad.
Why aren’t they in Fallout 4?
The Doylist answer is that they’re highly customizable, and so they have no canon appearance, personality, gender, etc. But in-universe? Something happened.
“Accepting outsiders like yourself has proven disastrous in the past.” - Kells
“I've seen other soldiers come and go. Some were brave, some were honest... hell, some were even downright heroic.” - Danse
“Every doctor I've talked to was worthless. [] I don't need them... I need someone like you.” - MacCready
When Duncan first got sick, “someone like you” would have meant the Wanderer. This suggests (to me) that they’re not in the Capital Wasteland anymore. But they’re certainly not in the Commonwealth either.
The weird thing is that the Lone Wanderer is all over this game - they’re the namesake for a male hairstyle, a perk, a DCR song, a motorcycle brand… and the codename of Deacon’s mission to save the Railroad from certain destruction by recruiting the Sole Survivor.
Someday We’ll Find It, the Deacon Connection
Oh yeah, I’m going here. Desdemona’s terminal entries confirm it was always Deacon’s plan to get you onboard and use you to destroy the Institute. There are Railroad lookout posts near 111/Sanctuary and Red Rocket, and of course he followed you in Goodneighbor, Diamond City, and Bunker Hill (at least). His court jester vibe hides it a bit, but he’s manipulating you more than he’s manipulating Desdemona in the intro scene. And do you notice he rarely gives you a firm verbal disapproval unless you’re hurting the Railroad?
What could have caused Deacon’s interest in you, unless he’s made the connection between you and the Lone Wanderer? He’ll vouch for you if you haven’t accomplished anything yet, or even if you’re a Brotherhood member. A Pip-Boyed stranger emerges from a vault in the middle of a crisis, gaining friends, skills, items, and special abilities at a suspicious rate? Probably with the same gender and playstyle as the previous one? Heck, when he first heard the rumors, he probably thought you WERE the Lone Wanderer.
There are other indications the Railroad has been in contact with them — Desdemona mentions the Capital Wasteland as their primary destination for synths, and Deacon references Harkness’s recall code. If you refuse to pick a codename, Desdemona even assigns you “Wanderer.”
So what happened, then?
I think the answer lies with the Brotherhood, specifically in Deacon’s hatred of them. Sure, ideology is enough to hate them for, but Deacon sure seems suspiciously happy if you nuke their base of operations. (Some of) his comments on that:
“The Brotherhood... well, I met them on an op in Capital Wasteland a few years back. But now with Elder Maxson... Let's just say, not a fan.”
“That bastard Maxson really screwed them up. The Brotherhood used to be the good guys. Well, goodish.”
[Who’s Elder Maxson?] “He’s a piece of work, is what he is.”
And on his time in the Capital:
“Did I ever tell you about the time I was in Capital Wasteland? Now there's a tale.”
“Capital Wasteland. Exports: purified water, some decent tech, oh, and an insane suicidal cult that worships radiation. Thanks, guys.”
“I miss Capital Wasteland. You can actually drink the water there.”
And a few lines I’ve decided (with no evidence) directly refer to LW:
“Last partner I had wound up going... well, a little insane. I think it was all my show tune medleys.”
[After Maxson orders you to hunt Danse down] “See? This is what the Brotherhood's really about.”
And my favorite: “I’ve been looking forward to kicking the Brotherhood’s teeth in. I owe them.” This line comes before Glory is killed, so he’s not referring to that. The Brotherhood only recently arrived in force in the Commonwealth. He’s talking about something that happened in the Capital Wasteland.
In early 2286, Deacon moves to the Capitol Wasteland for awhile, probably to get a face change and lay low for a bit. He contacts the Lone Wanderer, who has barely heard from the Railroad in nine years. They begin to work together.
(In context, this journal entry looks like he’s somehow gathering intel to predict when Vault 111 will open, but I can’t think of a way for him to get that information or know why it’s important, so I’m not going to believe it just yet.)
The Wanderer is still a knight, maybe a paladin. Maxson has been elder for 2-3 years and is monitoring the Institute. Meanwhile, the Lone Wanderer and Deacon are setting up infrastructure to receive escaped synths.
And then the Brotherhood finds out about one of the safehouses. With their limited understanding, they believe that the Institute is holed up there and attack. The Wanderer intentionally throws the mission — maybe disobeys orders, maybe downs a vertibird or collapses a subway tunnel, or maybe even attacks their brothers to protect the synths.
And, well-
Either they were killed, or they escaped court martial and execution by a hair’s breadth and fled the Capital, leaving Deacon to believe Maxson had them killed.
There you have it. That’s why they aren’t in Brotherhood dialogue or records. Their accomplishments couldn’t be recognized because they’re a traitor. And that’s why it’s personal for Deacon.