Please, please do not provide any huge spoilers in the replies (albeit this is the "spoiler" forum).

I have a question for those of you who have beat the main quest. I the leader of the Minutemen and a member of the Brotherhood of Steel. However, I just recently traveled to the Institute and met up with Shawn (I think, still a little suspicious that he's actually my son). Ultimately I think I'll be siding with the Institute but here's where my question comes in...

I never really told the Institute thus far "yes" or "no." I am, however, currently doing a quest where me and a Courser are to retrieve a rogue synth, so the Institute is obviously not hostile to me. When I eventually decide to fully join the institute (I assume I'll be given the chance again at some point), will it be at the expense of my membership to the Brotherhood, and possibly the Minutemen? To be honest a lot of people don't like having to choose, but I for one do. I think it adds much more to the game.

Side note/question. When traveling to and from the Institute do we simply use fast travel? Or is there some other way to initiate this in the Pip-Boy or somewhere else?

Again, please keep spoilers to a minimum in answering any of these questions. Thanks.

It will affect your relationship with the Brotherhood.

You are still on track to side with the Institute, the game is programmed in a way so that you will have to choose between RR, BoS, or the Institute, any faction you choose will require you to destroy the other factions. The MM is the only exception where you only destroy one group (I'll let you guess which one) and leave the other two alive. You will know when you will be forced to permanently join a group.

BTW, DO QUESTS FOR THE RAILROAD. They have the best armor unlock perk in the game.

You can only travel back and forth using the pipe boy.

If you do decide to side with the Institute, only the Minutemen will be left, so choose wisely. Minutemen ending gives an opportunity to keep all but the Institute alive, so that's something else to consider. And yeah, there will be a point in the Institute quest line where you will inadvertently make BoS and RR hostile to you, so tread carefully.

I hope none of this is considered a "spoiler" for you. Granted, I haven't beaten the game either but I've been looking around the forums and the wiki for a while now, since I have been wanting to make an informed decision on how I will beat the main quest with my characters.

Couple other related questions that I think I know the answer to but I just want to be sure.

If I do things that would seemingly go against the Institute such as giving the holotape that has Institute information on it to Sturgis or giving the Serum to (can't remember his name but starts with a V)... will those things cause any problems with my affiliation to the Institute?

Neither will make the Institute hostile. The same applies with all of the other factions that want you to use the holotape on an Institute terminal. Once you're with the Institute, the only things that make them hostile are actual quests from other factions later on down their questline that demand hostile action against the Institute.

BOS yes, Minutemen no.