By popular demand, and since this mod is now older, I have decided to write a walkthrough explaining exactly what you need to do to get the desired outcome you want. The mod (indirectly) alters how certain vanilla quests work and also adds new quests.
1. The Preparation
Make sure you have the mod installed and activated, I am not responsible for your failure to do so correctly. The mod works. If it doesn't, then reinstall the game and/or stop using crappy pirated versions. End of discussion.
In-game, the first thing you should know is that success requires high Charisma as there will be many speech checks. Nothing short of 11 points in Charisma guarantees complete success, unless you want to keep reloading saves.
If your intention is to replace Elder Maxson with a synth, then you need to have met and talked to Maxson during the Prydwen introductory quest Shadow of Steel. It's best to complete this quest, this is an early quest and will not make you hostile to any other faction. If you do not do this, you will not have the option to tell Father to replace Maxson with a synth later.
If you want to remain on good terms with the Railroad, don't attack them or commit any action that normally makes them hostile. Once you are hostile there is no turning back even if you reform the Institute on your own. Avoid bringing X6-88 to the Railroad HQ as he is a permanent enemy and remains an enemy to them even after the end of the game, and even after the reformation of the Institute. If he gets you into a fight and an important NPC dies, you will be blamed and become permanently hostile to the Railroad.
Do not become enemies with the Institute, there is no way to undo it once kicked out, you will not become Director, and you will not be able to reform the Institute.
Do not use the "setstage" cheat unless you really know what you're doing. Most likely, you do not.
Fast forward, if you want Z1-14 as a potential companion, you need to make sure your character has knowledge of him. This is done in two ways:
1. Formally join the Railroad as an agent before you visit the Institute and then do enough quests for them inside the Institute to meet Z1-14.
2. Don't join the Railroad at all, intentionally remain an outsider. In your absence, Deacon figures out who Patriot and his allies are (off-screen). You may be able to learn about Z1-14 if you pass some speech checks with Desdemona.
You must also remain non-hostile with the Railroad to keep Z1-14 as your companion.
About Virgil, if you want him as a companion, then you must not, under any circ*mstance, give him the serum while he's in his cave. Stall for as long as possible, but don't make him hostile or suicidal. For him to be your companion, he must remain a super mutant. Sometimes a vanilla bug will make him hostile, I don't have a solution to that, that's not the point of this mod.
If you want Danse's perk, make sure you get it before the vanilla quest Mass Fusion. Danse's attitude towards you will change drastically after that and the usual Brotherhood quests will become unavailable.
If you want Glory as a companion, she must survive, the Institute must be reformed, and you must remain on good terms with the Railroad. To make sure she survives, the Brotherhood attack on the Railroad HQ must not happen. Avoid progressing to that point in the Railroad questline, ignore any synths in the Institute that ask you to meet in your quarters. Instead, work with Father up to the point where he asks you to kill the Railroad leaders.
You will need to complete Mass Fusion to progress in this mod, which will make you temporarily hostile with the Brotherhood since you will need to betray them.
2. Things Get Interesting
Reach the quest End of the Line, but do not kill anyone in the Railroad. Warn Desdemona instead that the Institute wants to kill them, press her for more information about her plans, do not blindly agree with anything she says. During this conversation, End of the Line will be failed but don't panic, you will not be kicked out of the Institute. When she reveals she plans to blow up the Institute, convince her that taking over as Director is the smarter choice. There is a series of red speech checks here, come prepared. Don't be too aggressive as some failed speech checks may trigger the Railroad to attack you and make you permanently hostile. If you pass the speech checks, you'll get a new quest that wasn't in vanilla called The Long March Through The Institute. This quest cannot be immediately completed just yet.
Go back to Father and lie that the Railroad was destroyed. If the conversation ends, talk to him again. The next quest is Airship Down.
Talk to him yet again and insist that you will not destroy the Brotherhood of Steel, demand to replace Elder Maxson with a synth, that he's the reason why there's no peace. If you pass his speech check, he will agree and you will get a new quest Next Level Machiavellianism. Father will message the Robotics division and a synth replica of Maxson will be ready for the mission by the time you reach Robotics. Synth Maxson will give you a communication module, use it to contact the real Maxson and lure him to CIT to be killed and replaced. He will not come alone, be prepared for a fight. Some synths and coursers will help. Radio signals will be jammed off-screen, so don't worry about Maxson notifying the rest of the Brotherhood. He won't get the chance.
Do not, under any circ*mstance, kill Maxson outside of the scripted event that's part of this quest, it will not work. You cannot kill him on the Prydwen or before this quest starts.
If you want to regain your status with the Brotherhood and access to the airport settlement, convince Synth Maxson to reinstate you, otherwise you will remain hostile with the Brotherhood, including with Synth Maxson the next time you meet him if you ever revisit the Prydwen on your own.
3. Alternatives to Next Level MachiavellianismIf you don't want to replace Maxson with a synth, there are a few alternatives, assuming you've been playing other mods.
If Sarah Lyons has become Elder (Project Valkyrie mod), you'll be able to skip Airship Down. Talk to Father and complete the quest Thanks, Sarah.
If Danse has become Elder (Danse Dillema mod), you'll be able to convince Father and the SRB to just send an operative to reset Elder Danse. The new quest is called The Great Reset. Since you are hostile to the Brotherhood at this point, a courser will do it for you off-screen and you won't need to be involved in this mission. You must also convince the SRB representative to allow you back into the Brotherhood. By default, they will recommend staying away from the Brotherhood as you did betray them.
4. Reforming the InstituteTo accomplish this, you must complete the final Institute quest Nuclear Family. You can complete it with or without the mod Father Companion installed. Father will die (or alternatively leave the Institute if you cure him or infect him with FEV so he can overcome his cancer). You are now the Director and can complete The Long March Through The Institute. Talk to Liam Binet and he'll reveal Allie Filmore as a potential ally. Or talk to Allie Filmore directly, your choice. If you can't convince her to reveal her support for the synths, try again in a few days. Do not kill her (yet) if you can't convince her, you will fail the quest and later the Railroad will also turn on you. At this point, Underground Undercover (if it is still active) and The Long March Through The Institute will end and the quest Not My Director will begin.
Allie Filmore has summoned the entire Directorate and their right-hand men / potential successors. Basically all the important people in the Institute.
Your goal is to attend the meeting and get unanimous approval to free the synths and end the mistreatment of Commonwealth settlers. You will need to sit down and speak to Allie to officially start the proceedings.
The people in attendance are as follows:
1. Allie Filmore - Head of Facilities, no chosen successor
2. Alan Binet - Head of Robotics, no chosen successor
3. Justin Ayo - Head of the SRB
4. Alana Secord - SRB successor, Justin's right-hand woman, the actual Head of the SRB if Justin dies or is banished during Plugging a Leak
5. Clay Holdren - Head of Bioscience
6. Isaac Karlin - Bioscience successor, Clay's right-hand man
7. Madison Li - Head of Advanced Systems, only if she remains in the Institute
8. Evan Watson - Advanced Systems successor, Li's right-hand man
If you don't want to attend the meeting alone and want security to be present, you can request backup from Z1-14, X6-88, or even an entire squadron of Minutemen if you completed Old Guns, for this you will need to talk to Preston and finish the quest Instant Karma that ends with a large number of Minutemen being teleported all over the Institute and the coursers reprogrammed to stand down.
You can deal with the Directorate as follows:
1. Let Allie and Alan live, execute everyone else. Allie and Alan already agree with your cause.
2. Convince as many scientists as possible to reform, execute only those that can't be convinced or won't stand down.
3. Use the Minutemen occupation of the Institute as a show of force to get unanimous approval and not have to execute anyone.
4. Go red wedding on everyone. Execute every scientist present at the meeting, abolish the Directorate, become the undisputed dictator of the Institute, rule alone.
For options 1, 2, and 4, it's best to have light backup, Z1-14 and X6-88 will do just fine and quickly put down anyone before they even have a shot at attacking you. (Just don't give them ridiculously overpowered weapons that can start a massive NPC fight in the entire Institute. Rifles will do just fine.)
Note that executing everyone will make X6-88 consider you an incompetent Director, forcing you to abandon him as a companion or going against your principles and resetting him.
4. Convincing the Scientists1. Allie Filmore - already agrees with you at this point
2. Alan Binet - already agrees with your cause
3. Justin Ayo - can't be convinced at all unless you use the Minutemen
4. Alana Secord - can't be convinced at all unless you use the Minutemen
5. Clay Holdren - can't be convinced to free the synths, but you can pressure him to abruptly defect and teleport out of the Institute by threatening to have him executed for the murder of Roger Warwick, this requires a speech check
6. Isaac Karlin - use a speech check to confront him about the Roger Warwick murder, he will be pressured to agree to your demands and approve liberty for synths
7. Madison Li - give her Virgil's holotape, proving that the Institute is untrustworthy and Father was a liar, this will make her question the Institute's treatment of synths and their claims that synths are just lifeless robots
8. Evan Watson - he is a synth (non-canonical retcon on my part) grab Father's holotapes from his room exposing Evan Watson as a synth replacement of the real Evan Watson, use the tapes to blackmail him into stop being a self-hating synth
Conclude the meeting in any way you see fit. Not My Director ends in success, you'll even get a copy of the legal document granting synths equal rights.
5. The RestThe rest is pretty straightforward. After the Directorate meeting, you'll get a new quest Humanity's Best Hope, this merely involves delivering a speech to the rest of the Institute about the new change in policy towards synths and Commonwealth residents. Choose your words, then you get up to 3 more quests:
Stop the Presses - Involves speaking to Piper about the Institute's reformation, if she's still alive at this point.
Homecoming - Get Virgil back to the Institute, if he's still alive at this point. If he remains a super mutant, he will be your companion above ground and get a cool new super mutant suit. He won't accompany you as a human, too weak. Be sure to introduce him to Strong for some hilarious dialog.
Welcome to the New Age - Notify Desdemona that the Institute has been reformed. Or kill her to cut loose ends. Your choice. You won't get this quest if you're hostile with the Railroad and you won't be able to re-establish any form of dialog as you'll just be attacked on sight.
You can also notify Nick Valentine, Dr. Amari, and Irma off-quest.
You can complete all 3 quests or none, but the next time you visit the Institute, you also get the final cutscene, custom-made for the major choices made in this mod.
If the Brotherhood was destroyed the vanilla way, you will instead get a final quest called Mutually Assured Armistice. Meet with Sentinel Hill from the West Coast division above ground, agree to a truce with the Brotherhood, don't or just kill the entire delegation, your choice really. If you agree to a truce, the conditions will include a delegation of Brotherhood scribes as inspectors, monitoring the synth program. Okay, now return to the Institute and get your cutscene.
6. Another AlternativeIt's also possible to do this mod by focusing on the Railroad questline and putting the Institute questline second, however, doing so will get Glory killed and the Prydwen will be destroyed, no peaceful alternative to deal with the East Coast Brotherhood even if Sarah Lyons or Danse is Elder.
After you have destroyed the Prydwen, Nuclear Option will start. If you previously failed to convince Desdemona that her plan is stupid, you will get another chance here. Convincing her fails Nuclear Option and gives you The Long March Through The Institute instead. Progress with the Institute up to the point where Father dies/leaves, then read above.
