Shaun Shaun , also known as Father , is the son of the Sole Survivor and 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 . During the Minutemen / Brotherhood of Steel / Railroad endings , when the Sole Survivor can talk to Shaun on his deathbed , he remains convinced to the end that by destroying the Institute the they are making a terrible mistake , and is forthcoming in his bitterness at the turn of events . His parent can convince him to grant the access codes to at least partially disable some of the synth defenders fighting the player character ' s allied forces , assuming they pass the charisma checks , before he asks them to leave him be as his death is coming regardless of whether or not the Institute detonates . If this ending is taken and the young Synth is taken with them , the Sole Survivor will receive a holodisk recorded by Father after being interacted with . The synth Shaun tells the Sole Survivor " " I didn ' t listen to it , so I dunno what it says , but I think it ' s important " " . It is revealed that the young boy was reprogrammed to believe that the player character is their parent , as the first meeting between the synth and player character ( who was led to believe that the synth was their missing son ) caused the synth to become confused and call for help . The reason for him being reprogrammed is explained by the real Shaun in the holodisk , saying " " I would ask only that you give him a chance . A chance to be a part of whatever future awaits the Commonwealth . " " Appearances . Shaun appears only in " Fallout 4 " .