I hope you can help enhance my story experience. I'm stuck at some story point where I 'visit' the Institute and after, as the results/reactions of people just don't make any sense to me. I'm not asking you to lay out all the consequences of the decisions I can make here, but merely if there is more - if I missed something or if you could point me to a direction where I can at least follow the story with more sense.

I'm going to lay out my thoughts during the gameplay from the point I'm about to go into the institute and during the visit. ***Spoilers Ahead***

I'm leaning currently towards the Minutemen, annoyed with the BoS and skeptical/reserved towards the Railroad. I'm against the production of synths, reserved to synths, but neutral towards memory-wiped ones. I've completed all the faction's quests up to the point you had to go to the Institute and seen about 70% of the map.

After obtaining server data using the holotape and meeting Father. I had the urge to shoot him, not believing his story or intentions. (And if he truly did follow my progress, then I've been shot and opposed by the Institute enough in the Wasteland to know he doesn't care about me as much as he claims). As he merely asked to give the Institute a chance to explain their cause and let me decide later, I thought I could use that to my advantage to obtain the anti-FEV-experiment for Virgil (as promised) without having to shoot my way through. Also the chance that Father is truly my son kept me from pulling the trigger (if anyone would deserves to explain himself, it would be your own kid).

I explored the Institute and met the employees, keeping an open mind but refused to give them an answer on whether I'd join in or not. I even was glad not to shoot Father when I found the holotape of Dr. Lin, that tells you that Father broke research protocols by demanding a child synth (Shaun) for unknown reasons - even prioritized this over progress on Stage 3 (I thought of the possibility that he develops a child synth with his personality and memory to give me [the protagonist] a chance to make up for lost time with his son). The data in the Institute however, does show a very narcissistic Father, leaning even towards an early stage god-complex, rather than a very ambitious 'scientist' caring about humanity. The former FEV research lab confirms this, as it seems to prioritize fully anolyzing the creation / recreating a (better?) version of the FEV, rather than finding a cure - even sacrificing their own people for it.

After obtaining the experimental FEV cure I decided to get out of this place, preferably without hassle (for now). I walked up to Father and wanted to tell him that I've seen enough to disagree with his methods, or tell him I don't want to join in. However, this is not possible! Whatever I tell him (all the options seem the same with merely a different tone), he seems to ignore it regardless and even gives me an assignment! This is a MASSIVE jump from "please, look around first, then you can decide" in the last conversation I had with him.

I was a bit confused, but I thought this was just poor scripting. I assumed that I could just ignore the task. Upon leaving the Institute nobody seems to ask me "wow, you're alive, what did you find?!", my companion is just staring at me like nothing happened, and even worse: Virgil ATTACKS me when I tried to bring him the experimental FEV-cure.

I'm completely lost and clueless, while I was quite enjoying the story and read pretty much everything I come across not to miss anything. What went/did I do wrong? I know I can just start murdering everyone in the Institute out of the blue (without any dialogue), but I just can't believe that's the ONLY alternative in a Fallout game.

I pretty much did the exact same thing you did and was ready to verbally tell Father to take a hike. For some ridiculous reason, the only way to do that is by pursuing another faction. OR! You can play both sides and secretly pretend to be on father's side and but gain intel for the Minutemen or whoever.

But in regards to declining his offer at the point you're at now. You can't. And it was a little frustrating.

Thanks for your quick reply!

Did they adapt the dialogue to this - can you tell a faction you're infiltrating the Institute and play pretend? Because, like Virgil, some people are hostile all the sudden (HOW does he even know I, unintentionally, side with the Institute!? Why doesn't he even engage dialogue first, but just immediately attacks me?). Is the only way to stay on Virgil's good side to just start murdering everyone in the Institute? There is NO dialogue option in the Institute even to just engage combat.

Did you give the Holotape with the Institute data to your chosen faction? They DEFINATELY have a reaction to your infiltration.

You can just warp out of the Institute as soon as you get the transmitter attached to your Pip-boy, nothing's forcing you to do Father's quest. Even Father himself doesn't force you to do it when you talk to him, it's more like "Please do me a solid and take this job that will help you understand my side of the story".

Either way, both the Brotherhood and the Railroad want you to be "The Mole", so if you're doing anything other than making the Institute hostile at the first chance (by attacking bystanders in the Institute lobby, probably), you'll have to do work with them a bit longer.

As for Virgil being hostile, that isn't supposed to happen. Did you say something to piss him off or accidentally hurt him?

Weird.. I'm not sure why Virgil would attack you. I was able to give Sturges (I sided with the minutemen, initially) the holotape that I plugged into the institute terminals and then gave Virgil the data he asked for.

In terms of adapting the dialogue. They do. However it only happens when factions overlap. Sometimes you will be doing a mission for the Brotherhood of steel that doesn't involve the Institute and vice-versa. There is a point in the game where you do have to finally pick a side, and the game will warn you of this with a little dialog warning.

Thanks for the information, people!

I'm playing through the institute again. Picked up the experimental FEV-cure... went to Dr. Lin at the Advanced Systems department. Warped out. The holotape return caused indeed a positive response. However, I went to Virgil and -again- his sentries start blasting me upon entering his cave.

I've stolen nothing, didn't drop mines or accidentally jumped on him with my power armor... I really don't get it.

At least the institute story is continuing with somewhat more sense. I just hope that not being able to communicate with Virgil won't spoil my story experience any further.

Must have bugged out with Virgil there, sorry mate. That or you screwed up in some vague way.

Either way, he's not vital to the story after "The Glowing Sea" so don't worry about it too much.

That's truly a relief. thanks again.