This is a play-through guide not only for Project Valkyrie, but for all the quest mods in the so-called "Thuggyverse":

Fusion City Rising - September 2016 Mod of the Month
Outcasts And Remnants - April 2017 Mod of the Month Runner-Up
Project Valkyrie - August 2018 Mod of the Month (Requires Outcasts & Remnants)
Depravity - August 2019 Mod of the Month (Requires the asset files of Outcasts & Remnants)
Diary of a Madman - Shortcut to the vanilla main quest alternate endings offered by Depravity if you don't want to play that mod (requires Depravity + OAR)
Settler & Companion Dialogue Overhaul - November 2019 Mod of the Month
Commonwealth Bounties - Test version is playable via Discord, see commonwealth-bounties thread.

The above mods are fully compatible with each other. No individual mod requires the other mods in the series except as noted above.

With Project Valkyrie it is possible to achieve alternate endings to the vanilla main quest beyond what Bethesda intended.  At one extreme, you can kill Preston, Father, Maxson, Desdemona, and wipe out their factions. At the other extreme, you can help all the factions co-exist peacefully with each other.

With Depravity and/or Diary of a Madman, you can optionally do all of the following on your own without the help of any other faction:

- Blow up The Castle, kill Preston, and turn the Minutemen hostile against you
- Blow up Diamond City
- Blow up Railroad HQ
- Blow up The Prydwen
- Blow up The Institute

It is possible to make peace with all the factions in Project Valkyrie, then start blowing up any individual faction afterwards. If you're here for information on which order to play these mods, scroll down to the second-to-last green underlined topic: "Thuggyverse mods: Which order should I play them?".

There are 7 quests in Project Valkyrie's main story, weaving into the Fallout 4 main quest, which in chronological order are:

In a Darkened Room - Find a mysterious prisoner named Valkyrie and help her escape Parsons Insane Asylum
Malpractice - Help Valkyrie figure out why she was abducted
Heir to the Throne - Discover a hidden game-changer to shift the balance of power in the Commonwealth
Wag the Dog - Meet the B.O.G. Outcasts and help Sarah reclaim her position as head of the Brotherhood of Steel (or don't)
Break The Wheel - Help Sarah fight off a group of BoS insurgents
Peace Through Superior Firepower - Use Liberty Prime to retake Quincy and spread democracy throughout the Commonwealth
The Revolution Will not be Televised - Help a rogue scientist turn The Institute into a force for good, and become Director if you aren't already

Depravity's main quest arc consists of the following:

Murphy's Law - When you enter Concord, get to know a gang of Ex-Minutemen turned slave traders (Fallon Company)
Blood on the Highway - Help your new friends retaliate against the Gunners and steal their gear
Like a Goodneighbor - Clean out the Riff Raff in Goodneighbor (incorporates Silver Shroud, The Big Dig, and The Cleaner)
It's a Long Way to the Top - Secure the sniper perches overlooking Goodneighbor, and staff them with Neighborhood Watch
Building a Better Flophouse - Take out Marowski and help renovate Hotel Rexford
The System Has Failed - Unravel a nefarious Institute plot against the citizens of Goodneighbor and Diamond City
We The People - Defend Diamond City from an attack and blow up Gunner's Plaza in retaliation
Change We Can Believe In - Become mayor of Diamond City, and rule it for good or evil (e.g. allow ghouls back in, establish slavery, punish people, etc.)
The New Rexford Hotel & Casino - Take ownership of a renovated Hotel Rexford
Human Resources - Recruit staff and NPC's discarded by the main game to work and/or live at the Hotel

Depravity's vanilla main quest alternate ending arc starts with the following prerequisite quests:

Follow the White Rabbit - Help Raina at Fallon Company secure a stimulant supply for her new chem to compete with Jet
The One Who Knocks - Take out the rival gangs in the Commonwealth who are dealing Jet
Gone Shootin' - Protect the Fallon Company dealers, assassinate the remaining independent chem dealers, and take over Marowski's chem lab
Holding out for a Hero - Help Harley at Fallon Company deal with her troubled past
Symphony of Destruction - Help a disturbed kid at Fallon Company play out a revenge fantasy
Burn Them All - Help Stella find explosives to make more mischief

Once the above quests in green are complete, the alternate ending quests that follow are all OPTIONAL and can be done in any order:

Retaking Independence - Gain access to all the Minutemen perks (e.g. artillery) without Preston and blow up The Castle
Your Settlement Does Not Need My Help - Kill Preston and turn the Minutemen hostile
The Little Engine That Couldn't - Blow up Railroad HQ
Prydwenburg - Blow up The Prydwen
Fire on the Charles - Blow up The Institute
Can't We All Just Get Along - Deal with civil unrest in Diamond City, and optionally de-escalate or escalate the situation and blow up the city

If you want to play the above 6 quests without playing Depravity, install the mod Diary of a Madman and access the above quests via the holotape you find at Pickman Gallery.

There isn't a right or wrong way to play these mods. You can start regardless of what point in the game you're at or who you've sided with, although arguably Project Valkyrie plays better if The Institute and Brotherhood of Steel are still alive.

An RPG approach to Fallout 4

1) Don't define my character for me Bethesda. Let me be whoever I want.
2) Don't force irrational plot choices on me for the sake of creating conflict. Let me say "no", and let me do things for my reasons, not yours.
3) Let me skip over or alter the parts of the Institute and BoS main quest lines that don't feel right, to get the ending I want.
4) Provide a way to complete the game that doesn't prevent me from accessing faction-related quest content that I enjoy.
5) The settlement system is more fun when I discover things on my own and when I'm not in any way forced to interact with Preston to access settlements.

Example of what is possible

(Optional: Use an alternate start mod like Start Me Up if you don't want Bethesda to define your character as a parent searching for their kid)

Leave Vault 111, ignore Preston, meet Stella at the entrance to Concord, and start Depravity's quest line, going as far as you want- but don't start the alternate ending content in Depravity yet. You can also ignore Stella, explore the map on your own, and meet up with her whenever you're ready. Heather Casdin is a good companion to meet up with early in the game and help you explore the map.

While exploring, either before or after starting Depravity, meet up with Danse at the Cambridge Police Station, do the quest Fire Support at Arc Jet Systems, and agree to join the Brotherhood of Steel.

Also find The Railroad at their base and complete the quest Tradecraft with Deacon.

Interact with Preston if you want, but you no longer are required to. All the things he offers (his perk, artillery, Minutemen General outfit, access to all settlements, etc) can now all be obtained without him.

Once you feel like you've explored enough, head to Cabot House, read the desk terminal in Jack's lab, do the quests that lead to Parsons Insane Asylum, find Valkyrie, and let her quests, ending with "Heir to the Throne", ease things into the main game from there.

Before talking to Owen in "Wag the Dog" (Project Valkyrie), make the Prydwen show up via one of two methods:

1) Head to Diamond City, talk to Piper, rescue Valentine, let him help you find and confront Kellogg, exit Fort Hagen, and then the Prydwen arrives and the mod "Outcasts and Remnants" also starts if you're running that.

2) If running Depravity, finish the quest "Blood on the Highway" and talk to Murphy to get the quest "Where Oh Where Can My Baby Be?". This quest will optionally let you bypass rescuing Nick Valentine. You can find and confront Kellogg at Fort Hagen on your own, and you can side with him if you want instead of killing him. If you side with Kellogg, he will help you obtain a courser chip and the teleportation schematics you need to build the Molecular Relay.

The following are faction related considerations.

Brotherhood of Steel

At some point before heading to the Prydwen, meet Danse at the Cambridge Police Station and do the first few quests there (Fire Support, Call to Arms, Semper Invicta, and The Lost Patrol) as they're fun and add depth to the BoS.

Then once the Prydwen arrives, proceed with "Shadow of Steel", "Tour of Duty", and "Show No Mercy" to obtain access to the Prydwen's amenities and the Vertibird Signal Flares. The quest "Duty or Dishonor" can also be completed by talking to Kells at this point.

I don't complete "Liberty Reprimed" because near the end of the "Wag the Dog" quest it's possible to make Liberty Prime functional and take him as a follower by helping the BoG, so there's no need to help the BoS do it in the "Liberty Reprimed" quest. If you want to make Quincy a Settlement after you liberate it with Liberty Prime, download the mod City of Quincy - New Settlement.

Another reason not to complete "Liberty Reprimed" is that doing so will auto-start "Blind Betrayal", where you will potentially lose Danse or get forced into attacking the Railroad for no reason on the "Tactical Thinking" quest which auto-starts after "Blind Betrayal". Danse's companion perk, which isn't normally available until after "Blind Betrayal", can be added via console command: player.addperk 0008428d. That way it's possible to have Danse as a companion + his companion perk + the BoS won't shoot at Danse on sight like they will if you've completed "Blind Betrayal".

A more immersive way to gain Danse's companion perk (as of OAR v1.4) is to read the wall terminal in the Robotics Division of the Reformed Institute. This will start the quest "Breaking the News", where you inform Danse of his true identity, and have options to 1) Help him deal with it emotionally, 2) Kill him, or 3) Help him commit suicide. The companion perk is obtained if Danse is alive at the end of that quest.

You can play through the BoS quest line as far as you want, but after "Show No Mercy", I head to the BoG bunker to do the "Wag the Dog" quest, which ultimately lets leads to promotion to Sentinel and the opportunity to remove Maxson as Elder, either violently or via persuasion, or leave him in power by lying to Sarah (in which case Sarah will not become romanceable).

If you remove Maxson as Elder peacefully, you'll have an opportunity later on to help him redeem himself (as of OAR v1.4), and take him along as a fully-voiced quest-giving companion, once you become Director of the Reformed Institute.

If you decide to build the Signal Interceptor with the Brotherhood of Steel (instead of the Minutemen or Railroad) in the quest The Molecular Level, finish that quest before recruiting Owen in "Wag the Dog". If you choose to build the Signal Interceptor with the BoS, but then overthrow Maxson before building it, the BoS won't help you build it anymore, in which case access the Institute via Carter Beckett in the quest "The Revolution will not be Televised" (starts after "Wag the Dog") and "The Molecular Level" will then auto-complete.

Completing "Wag the Dog" provides access to the Brotherhood of Steel's resources and nearly all of their side quests, without needing to worry about them starting war with other factions that would prevent access to, for example, the Railroad side quests.

Railroad and Minutemen

These two factions are never enemies with each other, and they are reactive, meaning you can go as far as you want in the quests for either faction without being forced into a conflict with the Institute or BoS. It is only after being attacked, as a result of your progress in the Institute or BoS main quests, that these factions will initiate aggression against the BoS or Institute main facilities.

You can seek out the Railroad headquarters at any time and do as many quests for them as you want. Eventually, you will reach a point in the Railroad main quest "Underground Undercover" where the quest objective is "Continue Working with Father" because the game is waiting for your progress with the Institute main quest before moving forward with the Railroad.

Same for the Minutemen, by finding Preston in the Museum of Freedom. The Minutemen main quest eventually stops moving forward on its own until/unless you get banished from the Institute.

The Institute

Act 1 of the vanilla main quest ends with the aftermath of killing Kellogg at Fort Hagen.

Act 2 of the main story is about finding a way to access the Institute, through the quests Dangerous Minds (access Kellogg's memories), The Glowing Sea (meet Virgil), Hunter/Hunted (obtain a courser chip at Greenetech Genetics), The Molecular Level (use the courser chip and a relay to teleport into the Institute), and Institutionalized (meet the Institute and their department heads).

Act 2 lacks replay value because it is heavy on plot exposition and light on action. The second time you play through the main quest, you already know the secret that Act 2 reveals, and you may want to skip the grind in order to reach the point where the action starts back up and your decisions matter again.

If so, you can skip all or part of Act 2 by doing the quest "The Revolution will not be Televised", which Sarah gives you after completing "Wag the Dog", and letting the rogue Institute operative named Carter Beckett teleport you into the Institute, where you can remove whoever you don't like, grab your son (if you choose, it isn't forced), and leave, letting Carter and her conspirators finish the coup. Or just kill everyone, except Allie, as she's your ticket back to the surface.

You don't have to acknowledge that Father is your son, or that kid Shaun is a synth, or that you even have a son, if you don't want to role play that way. Nor do you have to sit through the Institute intro scene with Father where you're not able to obtain answers to the truly important plot questions. Although you can choose an alternate version of this scene later, if you want.

There's a cost to accessing The Institute this way - missing out on some vanilla Institute content, specifically:

Synth Retention: No retrieving Gabriel from Libertalia, but you can fight that battle on your own at any time.

Battle of Bunker Hill: A battle between the Institute, BoS, and Railroad where no one usually shoots at you and your choices don't ultimately matter.

Mankind Redefined: Attending a board meeting where all of a sudden you're going to be leader of the Institute. ???

Mass Fusion: Retrieving some tech from the Mass Fusion building. This is a cool world space, but you can fight through most of it on your own at any time, and if playing Depravity, the quest "It's a Long Way to the Top" will send you there and let you access the roof.

Pinned: Recruiting a wasteland scientist to join the Institute. Boring.

Powering up: Recording a radio message. Really boring.

End of the Line: Killing the Railroad, thereby denying you their side quests and ignoring that it makes little practical sense to kill Desdemona when you can just tell her that you're in charge of the Institute now.

Airship Down: Killing the Brotherhood of Steel. But what if you don't want to? Or not yet? Can still blow them up later for the Railroad.

A House Divided: Dealing with Institute Bioscience politics.

Building a Better Crop: Warwick Homestead. The secrecy over better crops is odd. Instead of simply offering a starving farmer a new crop that will feed his family, the Institute decides to replace him. ??

Plugging a Leak: Finding out who is freeing synths, which you already know once you've played through it the first time.

Institute radiant quests: Tissue samples, technical docs, and feral ghoul extermination. Project Valkyrie will later give options to do these types of quests via other avenues.

X6-88 as companion: He isn't available as a companion until after completing "Mankind Redefined", after which you can send him to whatever settlement you want.

To access all the vanilla Institute content, do the above Institute quests first, starting by teleporting into the Institute via "The Molecular Level", before doing the part in "The Revolution Will not be Televised" where you meet Dr. Zimmer and Carter teleports you in. Then proceed with "The Revolution Will not be Televised", so that as Director, you can actually direct the place.

After the Institute coup in "The Revolution Will not be Televised", you also have to choose how to deal with the Railroad and Minutemen, to make sure they don't still plan to blow up the Institute.  That can be resolved either peacefully or violently.

Following this scenario, here is what the game looks like at the end of the main story:

- The Prydwen is intact and available as a resource.  The BoS Leadership is either alive or dead depending on your choices, and you can keep doing side missions for the BoS.  You can also take Liberty Prime as a follower whenever you want.

- The checkpoints throughout the Commonwealth that spawn random battles are manned by the reformed Brotherhood. There will still be skirmishes between factions since, even though there is general peace, hate doesn't dissipate overnight, and certain members within factions will still lash out at each other.

- The Institute is intact and available as a useful player base and a source for new side quests. Also three companions: Synth Nate, synth Nora, and Gloria.

- Whether or not Preston is dead or in jail, you can still build settlements and help maintain/defend them independent of Preston.

- All the Railroad side quests are still available (unless you decide to kill them).

- Access to a bunch of quests through the B.O.G, Back Bay Players, and Natick Banks Raiders, as well as the companion side quests offered by Owen, Sarah, and Valkyrie, including the Sarah romance progression.

- Avoidance of certain plot points in the vanilla main quest that may hinder immersion or role play, or feel like a grind on a repeat play-through.

Anyway, that's just one way to do it.  There are scores of combinations to make things turn out differently. There are in-game warnings at multiple points in the mod letting you know if what you're about to do will change something in the vanilla main quest, and giving you an opportunity to hold off, so you don't miss any content that you want to play.

If you don't like the vanilla options for Father (death), or the Project Valkyrie options (death, prison, or ignore), and instead want Father to live and be a companion, then download Father Companion before finishing "The Revolution will not be Televised" and run Father Companion alongside Project Valkyrie. The mods communicate with each other (without any mod dependencies) for continuity of story.

Thuggyverse mods: Which order should I play them?

There's no right answer. The various mods are meant to complement each other and combined contain over 70 hours of content if you do everything once. You can generally play the stories in whatever order you want, or all at the same time.

Here's a suggested approach, if you're starting on a newer game with a low-level character:

1) Start with Depravity. Meet Stella outside Concord and do the quests "Murphy's Law" and "Blood on the Highway". That will give you a player base, access to side quests from a new faction, a dungeon to send annoying NPC's like Marcy Long to live in, and a couple companions to choose from. Get the next quests "Like a Goodneighbor", "Holding Out for a Hero", and "Where oh where can my baby be?" (if Kellogg is still alive) that Murphy, Raina, and Harley give you.

At that point you can continue with the Goodneighbor and Diamond City adventures: "Like a Goodneighbor", "It's a Long Way to the Top", "Building a Better Flophouse", "The System Has Failed", "We the People", "The New Rexford Hotel & Casino", "Human Resources", as far as you feel like going, until you become mayor of Diamond City and owner of the New Rexford Hotel & Casino.

If you want to find Shaun, proceed with the quest "Where oh where can my baby be?", and then decide whether you want to get into the Institute by killing Kellogg and helping Virgil, or by sparing Kellogg and using his expertise to bypass Dr. Amari and torture the needed information out of Virgil. That will take you through "Reunions" and all the way up to "The Molecular Level", and by then the Brotherhood of Steel will have shown up.

2) Then do Valkyrie's quests through "Heir to the Throne" + meet Danse and the Brotherhood of Steel and do their first few quests as detailed above. Also meet the Railroad and Institute if you want.

3) After interacting with the Brotherhood of Steel up through the quest "Show No Mercy", head to the BoG bunker. Complete the opening quest "Initiation" to gain access to the main bunker.  Then you have some options on paths to take:

- B.O.G main quest to fight the Enclave, infiltrate an underwater Vault-Tec bunker, and start a Teleportation Network (starting with "In Plain Sight" quest)
- B.O.G. side quests to hunt bounties, retrieve tech, kill Gunners, harass the Institute, or troll the Brotherhood of Steel
- Raider and time travel side quests from Sam and Dr. Brown at Raider Emporium
- Pimp side quests to help the Back Bay Players grow their influence via guns, drugs, bounties, and adult entertainment.
- Project Valkyrie main quest to take over the BoS with Sarah ("Wag the Dog") and/or take over the Institute with Carter ("Revolution will not be Televised")

4) Once you've interacted with the Railroad and Institute in your travels, start Fusion City Rising by talking with Peter at Railroad HQ. The Sword of Atom and Ini-Tec battles in Fusion City Rising are tough, and don't present easy opportunities to run away, so you might want to wait until your character is at least level 20 before attempting them, and higher is better.

More Options

If you ultimately want to side with the Enclave, then download America Rising, do the Enclave quest "In Plain Sight" from Outcasts and Remnants first, then do the America Rising quest to help rebuild the Enclave.

If you grab some other quest mods like Tales from the Commonwealth, 50 Ways to Die at Dr. Nicks, Lima Detachment, and Operation Wilkes Estate (to name a few), your play-through should feel much fuller and more satisfying along the way.  For an epic battle to top it all off, head to New York in Operation Manhattan, teleport Liberty Prime to you (via Project Valkyrie) and watch him square off against Gunner Liberty Prime (from Operation Manhattan).