A horribly transfigured Jeffrey Spender purposefully sheds doubts over his identity -- and over if he's Mulder himself -- breaks in the X-Files office and tries to gain the trust of Scully, Doggett and Reyes in order to reach William. He injects William with magnetite that rids him of any alien influence on his biology. Yet for the aliens William will always be their prophecised leader, so in order to protect his identity Scully resorts to giving William up for adoption.
With the final stretch of episodes, David Duchovny returns (for directing) and the promotion campaign makes sure that everybody knows that -- at the expenses of the two new strugging leads. Storylines are closed; after getting rid of the Lone Gunmen (9X15: Jump the Shark) and Doggett's son (9X16: Release), we are getting rid of William. Written by Carter, Spotnitz & Duchovny, the episode plays heavily on, once again, Scully's weepy feelings when she doubts whether the Breather is Mulder or not (exacerbated in the scenes where she examines him and they look close to kissing, and where the Breather is holding William and weeps).
Jeffrey Spender returns from the dead! After he was shot by his father in 6X12: One Son, Jeffrey survived and eventually came into the hands of doctors experimenting on him procedures for the conversion of a man into a Supersoldier: "a failed attempt to turn me into one of these alien men. I was a guinea pig, a test subject", "I was injected", probably with a gene 'therapy' treatment that was supposed to change his genome and be mutated into a Supersoldier. "It burned. Throughout my whole body inside and out."
Doggett conducts a DNA test and the truth is revealed: "The DNA's a match to Fox Mulder's." Scully: "DNA's what Mulder shared with Jeffrey Spender." We get the confirmation that Jeffrey and Fox are half brothers -- through a straight-out DNA test! This is not very subtle compared to all the teasing over who Mulder's father really is ever since 3X24: Talitha Cumi. In fact it's totally superfluous ever since the confirmation in 7X04: Amor Fati (but as 9X19-20: The Truth shows, repetition is not among the writing staff's worries). Jeffrey: "Half brothers raised apart, that's about all that Mulder and I ever shared." Whatever Jeffrey did, it was as a kind of a post-mortem revenge to his father: "he couldn't destroy the one thing I love most, my hatred of him."
The magnetite injection
Jeffrey reaches to William and accomplishes his mission: he injects him with "an unknown metal". After examination, the hospital doctor don't find anything wrong with him, nothing but "an elevated amount of iron in his blood". Jeffrey explains it's "a form of magnetite". This is the first time magnetite is actually referenced, but it's obviously the same compound that causes the death of adult Supersoldiers (9X08: Trust No 1). Magnetite is an iron oxide (Fe3O4) that is actually quite common in iron ore found naturally on Earth; as its name suggests it's highly magnetic. The form of magnetite Jeffrey refers to is most likely magnetite in a solution since magnetite itself is a solid ore that cannot be injected; the injected liquid has a silver colour, different from the red vaccine against the Black Oil. The iron in William's blood is from that magnetite.
Before the injection William is "part alien" and after this injection William is a "completely normal" human being. From 8X20: Essence we knew that William was conceived in a purely normal manner, and despite their past both his parents were entirely (genetically) normal human beings. Whatever alien part William had it came in after his conception. Indeed, through the tap water William was infulenced by the modified chloramine (9X01/02: Nothing Important Happened Today) while he was growing up, giving him alien capabilities such as telekinesis (moving the mobile).
The injection will protect him, it seems, forever from the chloramine's influence: "They'll always know what he was. They'll never accept what he is" suggests irreversibility, a permanence in William's 'immunity' to the chloramine's effects. A long-term protection thanks to a single injection? This is not unheard of: heavy metals and radioactive substances, though at small doses, have a tremendous staying power in the human body; unlike most organic material that dies and is replaced throughout the lifetime of the organism, such material clings on and can be the cause for disease. The magnetite could similarly stay in William's body and essentially protect him. And that's what causes wrath to the aliens. After the injection, he no longer has any supernatural powers (the mobile above his new bed doesn't move despite William's attempts).
Jeffrey calls this injection "a gift". He believes that he has succeeded in taking William "away from them", the aliens. Indeed, if the chloramine was to turn him into a Supersoldier and develop an alien conscience in him, automatically making him subservient to the Colonists, then the injection prevents William from ever becoming fully alien. The gift is free will: William will be able to choose between following the aliens or the humans. Again, the phrase "They'll always know what he was. They'll never accept what he is" suggests that with William, biology is not what is important -- indeed biologically he was the same as all the other chloramine babies (9X08: Trust No 1). If biology is what made William important then Jeffrey's injection would have made him totally useless to the aliens, yet "it'll never be over"! William's importance is symbolic, religious, shrouded in a prophecy that is set in stone; Scully was chosen to be the mother of their leader by one of the sacred Ships (9X11: Providence) and this cannot change. Biology is not important, what he stands for is.
Despite anything that may happen to William, "your son is the one thing the aliens need". The Colonists/Supersoldiers had left William in Scully's hands because she was the most appropriate person to take care of him (and after all all her movements were under surveillance, see Trust No 1), the Supersoldiers have better things to do than baby-sitting. Jeffrey put an obstacle to the aliens' plans, but they will still come after him to attempt to convert him to their cause -- this time with more violent measures, perhaps to replicate him the hard, 'non-organic', way (Jeffrey: "Look at me, what they did. Is this what you want for your son?").
Surely we haven't heard the last of him: the 12-ish year old boy (2012?) in season 9's opening credits is William!
[Scully's vision of Mulder: "We're both looking for answers."]
Jeffrey: "For a moment you believed it, that I was him."
Scully: "I never believed it."
Jeffrey: "You wanted to believe."
Jeffrey the Breather [about William]: "No, it's important I do this. I want to hold him. For Mulder."
Scully: "He didn't have a choice to come into this life. I don't have a choice about what he is or was. But I do have a choice about the life my son will have. And shouldn't I choose that he never have to be afraid of anyone or anything? And can I ever really even promise him that?"
Reyes: "But who can?"