Shaun

Status: Deceased 
“At that time, the year 2227, the Institute had made great strides in synth production. But it was never enough. Scientific curiosity, and the goal of perfection, drove them ever onward. What they wanted was... the perfect machine. So they followed the best example thus far - the human being. Walking, talking, fully articulate... Capable of anything.” — Shaun discussing the creation of the Gen 3 synths with the Sole Survivor.
Shaun, also known as Father, is the son of the Sole Survivor and is the leader of the Institute in 2287. He serves as the primary antagonist of Fallout 4 unless the player character chooses to side with him.
Background Shaun was less than a year old by October 2077. On October 23, during the outbreak of the Great War, his parents took him and fled to nearby Vault 111 as the atomic bombs began to fall on the Commonwealth. Unaware of the true purpose of the Vault, Shaun and his parents became frozen in cryogenic suspension. Approximately six months following their internment, a revolt occurred and the staff abandoned Vault 111, leaving behind those frozen within, completely unaware of what had occurred.
The cryogenically preserved Vault participants remained undisturbed for around 150 years until the Institute discovered records regarding Vault 111. At this time, the Institute was desperate for genetic material unaffected by the radiation-ravaged wasteland for their Third Generation Synth project. The infant, Shaun, represented the perfect source of uncorrupted DNA, and the Institute set about to acquire him.
Sometime in 2227, the Institute dispatched their mercenary, Conrad Kellogg, to Vault 111 to retrieve Shaun. Along with two Institute technicians, Kellogg revived Shaun and his parents. The parent holding Shaun was unwilling to part with their son and resisted Kellogg and was shot and killed. Kellogg then returned the other parent to cryogenic suspension and terminated the life support of the other frozen Vault participants. Shaun’s surviving parent, who later becomes known as the Sole Survivor of Vault 111, would later escape the Vault in 2287.
Shaun was then raised by the Institute as one of their own, later nicknamed "Father" for his role in providing the DNA required to complete the third generation synths. In time, he became the acting director of the Institute. The Sole Survivor can find Shaun and can choose whether or not to side with him.
Shaun is convinced that the Institute is the only hope for humanity and tries to subtly convince the Sole Survivor of this. He gives them nearly unlimited access to the Institute, introduces them to the personnel of the Institute and even trusts them with missions to seek out and retrieve rogue synths. His feelings about the Institute as the future and last hope of humanity are mildly fanatical; he possesses an irrational fear of the surface and the potential threats of the Commonwealth to the Institute. Ultimately, Shaun wishes to take humanity further underground and away from the radiation, mutant, and danger-infested surface world.
However, Shaun does not require the rest of the Institute to adhere to his personal beliefs. In contrast to his contempt towards people above, he is not only open to recruitment of talented individuals, but allows them to gain high positions, like with Madison Li. He also does not seem to mind if his parent disagrees with his stances - as long as they don't endanger the Institute - and continues supporting them as their heir for as long as they are loyal to the Institute. Should the Sole Survivor, during the quest Nuclear Family, tell them that they don't believe that they can take his place, Shaun encourages them to create their own place rather than follow in his footsteps.
Having been raised in and by the Institute rather than by his parents, Shaun mostly lacks compassion - though he has a strong desire for humanity to survive - and seems indifferent upon remembering the death of one of his parents. He refers to the "incident" as "collateral damage" which potentially angers the Sole Survivor, though Shaun does offer that he has had his whole life to come to terms with that information. However, despite this indifference, he never lets go of hatred towards his parent's murderer, Conrad Kellogg, whom he does not forgive even if the Sole Survivor does. Interestingly, he does occasionally show some compassion. For instance, he apologizes to his surviving parent for the Railroad's destruction, which he does even if the Sole Survivor destroys them before Shaun orders it.
He also reveals it was his personal choice to awaken the Sole Survivor from cryostasis, not an error of Vault 111. He struggles somewhat with being reunited with the Sole Survivor in the Institute, ironically seeing one of his parents 'younger' than himself and wondering what they could have shared if the circumstances had been different.
It is later revealed that Shaun has a very aggressive form of cancer and one of the endings is for the Sole Survivor to take Shaun's place as director of the Institute upon his death, which was his primary wish all along.