I've been mulling this over for a few weeks, and there will be a TL;DR at the end.
I think, by making Kellogg a much more dangerous foe (and expanding out from that concept), it fixes a lot of the weird issues I had with the narrative of Fallout 4. Bethesda clearly wanted to go a different direction with this game, and that's fine with me. But giving such an unavoidable motivation (kidnapped child) limited role-playing options significantly. Fine, you can RP a shitty parent, but the real RP was a bit too meta for me – are you new to the series (main quest is urgent, get to it quickly), or are you an experienced wastelander (that main quest will wait, what's in that building over there?). It felt like a half step, and I think by making Kellogg the final boss solves that issue not by reverting to what Fallout is known for, but by leaning in and embracing the new direction for the story.
In the actual game, you find out the bombs are dropping, run to the Vault, narrowly avoid the blast that creates the Glowing Sea, get iced, wake up and watch your (I played Nate first playthrough, so I'll be using that as a reference) wife get murdered and your baby kidnapped. The killer stares you down as you get iced again, then you wake up again, get out and discover the Commonwealth. That all takes, in your mind, about 2-3 hours. Keep that in mind. From there you become the leader of a local militia, kill Kellogg, use his brain to access a hidden thinktank and research lab, meet some steampunk technofacists and a modern Underground Railroad, and eventually decide who is gonna take over the Commonwealth (for now). By the end, everyone kinda looks foolish and helpless compared to the guy who just essentially time-travelled 200 years into his own future. Instead, I want to shine up Kellogg. I want him to be extremely dangerous. "I've been alive in the Wastes for 100 years because I'm a goddamned cyborg" dangerous.
In the first "act" (Sanctuary to Fort Hagen), 4 changes come from this. First, I want Nate to actually reference the fact that his wife was murdered in front of him. I mean, it's a little disturbing that Nate's grieving period for his slain-in-literally-cold-blood wife lasts about as long as it takes to loot her corpse. Instead, make that half his motivation. Instead of "I'm looking for Shaun", Nate is "looking for the man who killed my wife and stole my son." Vengeance is a powerful motive, and we can use that here. Have him mention it to Preston, Danse, Nick, Piper, etc.
Second, you are not the General of the Minutemen. I mean, in game you aren't anyway. Not really – Preston names you General, then goes "oh, and we need beds, food, and water, defense would be nice, our old Fort back (don't mind the sea monster), this creepy old house would make a nice settlement don't you think, and that settlement you set up yesterday? They are already requesting assistance. General." So, for reasons that become clear later, we just skip that. Preston is the General of the Minutemen, you are simply enlisted. Maybe Colonel or something.
Third, Kellogg is something of an urban legend. The name is known, but details are scarce, contradictory, and exaggerated. Some say he's a Pre-War ghoul with half a face, other claim he's a prototype synth. Some even say he's an intelligent Deathclaw that learned how to use weapons. He's either 60, 110, 240, or an immortal vampire. He's fought three Deathclaws at once, or was it four? Nick says he's heard just about every story out there, and only two things are consistent – that he has been around for a long time, and he is incredibly dangerous.
Fourth, and this is the first huge change, the fight at Fort Hagen never happens. You fight your way though fewer synths, but they are noticably stronger and uniquely named/visually distinct. Kellogg's Synth, or Synth Assassin, or Modified Synth, something to distinguish them from the synths you may have encountered with Danse or in random exploration. They use plasma or laser weapons (perhaps even traditional ballistics), not Institute weapons. The whole time, Kellogg is talking shit over the intercom. He says he's surprised we were dumb enough to track him, but it's his own fault for getting sloppy. He dismissively refers to Nate as "the loose end" – that if he would've been allowed to run the op his way, there wouldn't have been a loose end to tie up. He thanks you for coming to him – saves him the trouble of tracking you down.
After getting through the (maybe 3 or 4) upgraded synths, you walk down a hallway to a locked door with a small window in it, and Kellogg walks up to talk. A twisted mirror of the murder of your wife. He says something about how, given that you got through his synths, you've shown you deserve your chance at vengeance. You ask him if that means he'll just let you kill him.
"Oh, no, I said "chance". Make no mistake, I'm going to open this door, murder you where you stand, and reunite you with your wife. This is where you get tied up, Loose End." click as the door unlocks. Suddenly, from the edges of the screen a blue light fills your vision and Kellogg, taken aback, chuckles "oh, this just gets more and more interesting. See you soon." You are teleported off into the room where you meet synth Shaun and Father.
From here, the story beats are largely the same. You find out Shaun is Father, he tells you about the Institute, and so on. He does point out that Kellogg is a necessary evil for them – he is ruthlessly efficient, especially after being cybernetically enhanced. I'd also like Kellogg to have been a primary consultant on the Courser program, helping them develop the best synth hunters possible based on his own experience. As payment for helping them, the Institute provided him with an endless supply of earlier synths to experiment with (hence the new armor, weapons, tactics, etc. of the synths in Hagen), as well as further cybernetic mods. Father understands your anger, but for now Kellogg is off limits. He's too valuable to the Institute and, frankly, you wouldn't have stood a chance against him.
Once you teleport out of the Institute, the Brotherhood of Steel float in and park at Boston Int'l, just like they do after exiting Hagen. Now, you spend the next third of the game getting to know the 4 big factions. You work for the Minutemen and take back The Fort. You help Deacon and the Railroad get back into Slocum's Joe. You meet up with the BoS for some nostalgic Mutie Massacre. You do… Institute things. They are all interviewing you as a potential recruit/asset, but you're interviewing them too. Who is your choice to help you track down and kill Kellogg once this is over? Do you go with the Minutemen for the wide coverage of their settlement network? The Railroad for their expertise in hiding their tracks (and thus spotting others' hidden ones)? The Brotherhood for their military might? Or perhaps the Institute, for their intimate knowledge of his missions, preferences, habits, and abilities?
The finale changes a bit based on who you pick. If you side with The Institute (which you are decidely NOT the new leader of), you have to take out Kellogg before ambushing the Railroad or the BoS. He's gone rogue; he's further augmented himself, beyond what the Institute did. His synths have been even further customized, making them stronger, faster, and harder to defeat. And he is looking for a way to take over the Institute himself, so that he can begin mass-producing synths for his army. He's gone to ground, and after reviewing some of his mission logs, you believe he is somewhere in the Glowing Sea. You take him out (with a group of friendly synths to assist), then the opposing factions. If you side with anyone else, you take out the Institute first (after copying date from their network onto a holodrive in an earlier mission). You find the logs and go after him accompanied by either a couple of Paladins, some Railroad operatives, or a mass group of Minutemen.
Why the changes?
Nate gets to feel more human. He seeks revenge for his wife the entire game, and that provides motivation to work with all the other factions. He's no longer the guy who woke up 2 weeks ago and managed to break into the Institute. He's just skilled, ex-military, and determined. And in the Wastes, that is ALWAYS a desirable person. It also gives a solid reason for Nate to work with any of the factions; "I'm chasing this guy. I could use some help."
Kellogg is now a key figure in the Commonwealth. He's an incredibly dangerous individual aided by technology, experience, and general mystery surrounding himself. He is a legitimate threat to you and any faction he comes up against, and taking him out feels like ridding the Commonwealth of a supervillain instead of just putting an aging merc out of his misery.
The Institute don't look like the kind of scientists who would have an admin account username:admin, password:password. Nate is 200 years behind the 8 ball, not a super genius, and has only been at it for a few weeks. Finding the Institute should be next to impossible. Instead, the Institute does what Kellogg actually says in the game – you don't find them, they find you. They maintain control the situation and come off even more ominous for it.
It also provides a clear moral quandry – who do you side with? The Institute are sociopathic and the cause of all your pain, but also the most qualified to track down the man who pulled the trigger. The BoS are single-minded and smell strongly of dangerous facists, but they also have the military skills to conduct an operation against an entrenched enemy. The RR and MM are both morally less questionable, but aren't well-suited to the kind of battle you want to drag them into.
TL;DR Kellogg is super dangerous. You meet him, but don't fight him at Fort Hagen; instead, the Institute kidnaps you and tries to recruit you as a second surface asset. Work with them or don't – either way, he attempts to build an extremely potent synth army, and you have to stop him with the help of whatever faction(s) you choose to work with. You get revenge for your wife and son and have a reason to side with the factions other than "I'm bored and agree with your philosophy". You are not the General of the Minutemen, nor are you named the new leader of the Institute. You are just a man on a mission.
What do you guys think? Did I create some larger hole in the plot that I'm missing, do you think you can improve it? I'm curious to see what everyone thinks of it. I liked Fallout 4, and I don't want to come off like I think I'm some genius game writer. I have the benefit of hindsight, the freedom from stress, studio demands, and game constraints. I just did this as a thought experiment. Let me know what you folks think.
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