The Concerning Storyline That Was Never Fully Resolved On Bones
Even though "Bones" featured new and exciting cases week after week for twelve seasons, the chemistry between forensic anthropologist Dr. Temperance Brennan (Emily Deschanel) and FBI Special Agent Seeley Booth (David Boreanaz) is what kept viewers coming back for more. The show skillfully crafted their partnership, creating a palpable will-they-won't-they tension that makes you constantly wonder why they won't set logic aside and just kiss already. The scientists at the Jeffersonian Institute worked tirelessly to solve crimes, but the true nature of Booth and Brennan's relationship was the real mystery.
Despite the show's scientific foundations, there are a few storylines that make no sense, like the dreaded Gormogon (Laurence Todd Rosenthal) arc and the controversial Christopher Pelant (Andrew Leads) saga. The series does a pretty good job of keeping the characters consistent, but any show that airs for so many years is bound to have a plot hole or two. "Bones," for its part, definitely introduced at least a few storylines that are never resolved, although they mostly concern minor characters.
However, there's one major plot point in Season 4 involving a main character that vanishes without a trace, never to be referenced again, even though it should've played a big role in the narrative.
Booth's memory loss is never addressed
In the Season 4 episode "The Critic in the Cabernet," Brennen announces that she wants to have a baby, a decision that comes as a shock to everyone at the Jeffersonian. Even more surprising is that she wants Booth to be her sperm donor, a contribution that the agent is naturally apprehensive about. It's beyond clear that the pair have feelings for each other at this point, but Booth agrees to donate a sample despite his reservations. His anxiety ultimately manifests as a hallucination of Stewie Griffin (Seth MacFarlane) from "Family Guy." Stewie even follows Booth into an interrogation, which finally alerts Brennan that something's wrong.
This isn't a one time occurrence. After being kidnapped by the Gravedigger (Deirdre Lovejoy) earlier in the season, Booth imagined that he was speaking with an old friend from the military who died. An MRI shows that he has a benign brain tumor. Under anesthesia, Booth has an elaborate dream where he and Brennan are married night club owners, but when he wakes up he seemingly can't remember who she is. It's a dramatic conclusion to the season, although it doesn't amount to much.
When Season 5 picks up a few weeks later, Booth is pretty much back to normal. His memory loss is never mentioned again, even though it clearly upset Brennan. It's one of the show's more ridiculous storylines, managing to negate an interesting narrative without advancing the plot in any way.