What network series finale would be complete without grandiose speeches and references to previous episodes galore? The “Bones” finale, “The End in the End,” managed to take down two birds with one stone in that regard. As Booth delivers a big ol’ affirmation of his love for Brennan (comforting her in the wake of the brief brain injury she sustained from their base of operations, the Jeffersonian, being blown up, which impeded her ability to take down Gerardo Celasco’s big bad Mark Kovic), he reminds her, “And besides, we’re way better than Mulder and Scully.” Still distraught, she, of course, replies, “It’s not their fault Chris Carter mucked up the revival” “I don’t know what that means.”
Much like the decision to blow up the Jeffersonian, this callback was largely done at Boreanaz’s behest. As then-showrunner Michael Peterson explained to Entertainment Weekly upon the finale airing in 2017:
“The Mulder/Scully line that Booth alludes to in [the finale] was absolutely David. He was like, ‘Yep, we gotta do it, we gotta do it.’ And there were moments when we were like, ‘We want to be humble, we don’t want to compare,’ and he’s like, ‘It’s a joke from the pilot. You gotta do it.’ And I think at the end of the day, he was right. We certainly didn’t want to throw any shade on anybody else. But I think it worked at the end of the day, and it’s funny for those fans who remember the callback to that very first episode.”
To be sure, “Bones” fans undoubtedly got the joke right away and it’s highly unlikely anyone else took it as a challenge. There’s plenty of room for multiple memorable investigative will-they-or-won’t-they pairings on television.