How can you turn down Deacon?
I played a super neutral human being. Told only people about Shaun if there was no other choice, being very secretive about everything.
He could be Shauns father or he may have had a short curcuit and believes he is the man, he got actual send to kill as an Institute Courser.
At the time you have to ask the Railroad for advise (sent by Dr Amari), you know these facts:
1. Institute kidnaps people and replaces them with Synths.
2. Institute killed settlers and burned down settlements.
3. Institute took your son.
4. Kellogg killed your wife, hired by the Institute.
5. On the mission to find the chip, you will meet a Synth being held prisoner by the Courser and I usually rescue her/it.
6. You whitness humans killing each other in fear the Institute replaced them.
7. You may meet friendly Synths in the Commonwealth, asking for the way to Bunker Hill.
8. You will see the BoS the first time, 'invading' ("Do not be afraid, resitance is futile" from those loudspeakers) when you leave Fort Hagen after killing Kellogg. (or you are introduced earlier, if you meet Paladin Danse)
9. You know about the MinuteMan from Preston.
If you turn down Desdemona and say you would not die to protect a fellow Synth fighting by your side, Daecon talks to you and asks if you would join anyway to fight the Institute.
I didn't turn down Deacon, checked on the BoS or helped the MinuteMan for now. Using the bat file from the mod "Factionless Institute", I am now at "Institutionalized" without faction. As a matter of fact, I think my whole role over.
Maybe I am a rogue Courser fighting with the Railroad? But this would not make sense, me dressing Mama and Stafford in Institute JumpSuits while they do the crops or trying to populate the Commonwealth with Synths.
From the first play, I know you potentially take over the Instittue and may be able to change things for the better. But you do not know that yet and you do not know your son is leading the Institute.
I will leave this whole thing for now as it stands and build up my own Cyborg army in the Sanctuary doing side quests.
p.s.
Since Shaun (the real one) got the Synth Shaun created from his organic material (as any Gen3+ Synth), put a lot of efforts and Institute resources into the project. He asks the character to take the Synth Shaun with him and treat him as his son, maybe even love it like it was his real one. This is supposed to be the most advanced model after all and could go for a clone of the old Shaun? The ultimate goal of the Institute seems to replace every single human with such a model?