Why Did Scully Give William Up For Adoption On 'The X-Files'? She's Still Conflicted About The Decision
Halfway through the The X-Files revival, there's a character whose presence has affected many aspects of the plot — but he has yet to make an appearance. Mulder and Scully's son William has been a frequent topic of conversation and a source of mystery and speculation — and there are plenty of questions about him, but seemingly no answers. The agents have repeatedly referenced that they gave up custody of child in order to protect him, but if you're new to the series, your memory is rusty, or you chose to sit out Season 9 (because, let's be honest, the show was not the same without Mulder), you're probably wondering exactly why Scully gave William up for adoption on The X-Files.
In "Founders Mutation," Scully tells Mulder that she sometimes hates herself because she "didn't have the courage to stand by [William]." With all due respect to Scully, years of guilt and doubt seem to have clouded her ability to assess the situation. Due to his parents' jobs and the fact that he possessed supernatural abilities, William was in grave danger before he was even born — and a number of traumatic events preceded Scully's painful decision to give him up for adoption. Plus, although Agent Reyes was an ally and a close friend throughout the ordeal, Scully really had to make the judgement call on her own because Mulder was in hiding and therefore the pair's contact was extremely limited.
Let's recap all the insane events that preceded Scully's decision:
The Birth Itself Was Traumatic
I've never given birth, but I would imagine that having a baby delivered by your colleague while a room full of super-soldiers watches is not exactly the scenario any woman dreams of. Scully and Reyes traveled to a remote area of Georgia for the birth, but they were followed by super-soldiers who seemed determined to take the child. They witnessed William's birth, but left without attempting to kidnap him. When Scully expressed confusion about this, Mulder suggested the baby wasn't what they thought it was — but that didn't make him any less of a miracle. Still, Scully remained unsettled and fearful that William would be targeted again.
He Exhibited Supernatural Abilities
Both Scully and Reyes witnessed William's supernatural abilities on multiple occasions. Viewers and Scully saw him apparently use telekinesis to move the mobile above his crib several times. Later, Agent Comer gave Scully an artifact from an alien spaceship, which she put in a drawer in her apartment. She and Reyes heard it rattling and moving on its own, and when they opened the drawer it flew directly to William's crib and hovered above him. Although she didn't exactly know what it all meant, it became clear to Scully fairly quickly that her baby wasn't ordinary.
His Life Was Repeatedly Threatened
William was targeted and put in grave physical danger multiple times throughout Season 9. In the episode "Trust No 1," an alien super-soldier cornered Scully and William in a rock quarry and told Scully that either Mulder or William needed to die. She escaped with her child after magnetite in the quarry killed the super-soldier, but the terrifying events continued. While Scully's mother was babysitting William, Agent Comer broke into the apartment, attacked her mother, and would have suffocated and killed William if Scully hadn't shot him first.
He was also targeted by a cult that believed that William was destined to "lead" alien colonization of the world. Scully temporarily sent William away with the Lone Gunmen in an effort to protect him, but their vehicle was hijacked by a cult member who kidnapped the baby. Scully, Reyes, and the Lone Gunmen worked tirelessly to rescue William, but Scully privately met up with Josepho (the cult leader) when he contacted her. He claimed he wanted to protect the child, but he refused to let her see William until she "brought him the head of Fox Mulder" to prove he was dead. After the Lone Gunmen successfully tracked down William's whereabouts, Scully and Reyes ran to his rescue and found him lying in a field crying but unharmed.
So, although William escaped death multiple times, it was a reasonable assumption that he would constantly be at risk because so many people had motive to take him. Even after Spender seemingly deactivated William's alien DNA, he warned Scully that the government would continue to stalk the child and attempt to reactivate his alien genes. When she gave him up for adoption, Scully somberly concluded that "they'll never forget what he was," indicating that she felt her child would always be at risk and her best hope was to send him to a place where he'd been infinitely more difficult to trace.
The main reason William's adoption could be problematic is that, despite the deactivation of his alien DNA, William is potentially still traceable in some other way — and, if he's found, his adoptive parents will have no idea how to protect him. William would have been extremely easy to find if he'd been raised by Mulder and Scully (she can always be tracked due to the implant in her neck), but the upside would be their knowledge and skills could help keep him safe even if they were all constantly at risk. However, William would have had absolutely no chance at a normal life if he'd stayed in his parents' custody and Scully took that into account when she chose to give him up for adoption.
At the time, she made the best decision she could. Scully is basically the epitome of strength and resilience, but she was physically and mentally exhausted throughout Season 9 — she was working long hours at a stressful job, caring for William on her own, and plagued by constant fears that Mulder had been captured and killed. Plus, she didn't exactly have a lot emotional support aside from Reyes. Given her mental state and the sheer number of traumatic events that occurred in a short period of time, it wasn't an ideal time for her to be forced to make such a life-changing choice — and that's probably contributed to her constant doubts about the decision.
It's interesting that, during the revival, Mulder has held back from expressing his emotions about William — because, in most scenarios, he's the more emotional of the two. After he told Scully that he thinks of his son but has moved on, his fantasy sequence about raising the child told viewers that wasn't the case at all. But, looking back at the series finale "The Truth," his reasoning becomes clearer. When Scully first told Mulder that she gave up William, one of the first things she said was that she was "so afraid" he could never forgive her. He immediately responded that she had "no choice" and he fully supported her decision, but Mulder surely hasn't forgotten her words and doesn't want to add to her guilt and grief.
Scully can openly second-guess the decision because she's the one who made it — and Mulder may share her doubts about whether or not it was the right choice. But, telling her that would be devastating and imply that he blames her. One thing is clear from their fantasies — both parents are worried that William is not as safe as they originally believed, and if the government does find him, they won't be there to protect him. Since William has managed to play a central role without actually having any screen time, I desperately want to believe that Mulder and Scully will find answers, closure, and peace before the revival concludes.