First off, I want to start with that I am not English/American , so English is not my primary language.

Second, I`m not entirely sure if there is another thread like this one on here, so if there is - please excuse me, and if you could also direct me to the existing one (if it answers my questions).

Ok guys, I've been playing for a while now (PS4 if it makes any difference) I'm 28th level right now, and recently I just went into the Institute. I did so with the help of the Railroad. Previously I became good friends with BOS and Minutemen (The Minutemen don't really bother me here). What's going right now with my storyline is so very confusing. All problems come from the fact that I`m friends with 3 factions, all of which have different and opposite morals and goals. So the thing is - currently I`m trying to free Synths from Father, while at the same time helping Father get back escaped Synths..

I had to do the Bunker Hill quest for Father, which was basically go and get some escaped synths and bring them back to the institute. The game gave me the optional choice to warn either BOS or the Railroad about this attack. As I haven't decided yet which faction I want to leave, I decided to warn the Railroad. I spoke with Desdemona and she told something kind of like " We are going to have to kill the Courser when he is with you, and that Father won't suspect me of surviving cause I was very tough. So I went to Bunker Hills where the Courser was waiting for me and we went to the site where the synths are. There were Synths, Railroad militia, BOS and The Coarser... And ALL of them were my friends... So what do I do in this situation ?! I came there to bring back the synths but also to kill the coarser. But all of these people are enemies between each other, so how can I take a side in such a fight? If I bring back the synths Im good with the Institute but the Railroad will hate me and BOS too...and other similar situations. So I killed the Courser cause there were no other Institute witnesses around, and because I guess this was the reason I warned The Railroad about the attack on the Synths in the first place.

The game then told me I had to go speak to Father about what happened at Bunker Hills and "Take care of the remaining synths", which I'm not sure what exactly meant, so I just left the battlefield (where synths, BOS and Railroad were still fighting each other ) and went to talk to Father. The map shows me he is near CIT Ruins and not in the Institute , which seems kind of odd since he`s never been above ground and also I can't find him there.

My real question here is - How should I proceed and what consequences will my decisions have on the game? I can be on all teams only until a point , at which I will have to become enemies with at least one of the factions.

There is no consequence for other factions. It's an Institute quest, so the only consequence would be if you betray the Institute and doesn't bring back the synths. You have to lie to Father and pass a really hard speech check if you don't return the synths and kill the courser. If you don't have high charisma, just return the synths for Father. It doesn't have any long term consequence unless you betray Father and fail the hard speech check which will block you out of Institute and Railroad questline completely. It's depending on whether you want to take that risk.

You can only be on everyone's team up until a point, they will talk about how you will become enemies with a faction if you proceed with a certain quest, Mass Fusion for the Institute, Spoils of War for the Brotherhood of Steel, Tactical Thinking from the BoS will require you to kill the RR.