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Fox's Bones recently came to an end after a whopping 12 seasons of action, adventure, and investigations... but not without taking a final shot at its spiritual predecessor, The X-Files. In a scene in which Brennan was feeling pretty down in the dumps, Booth tried to boost her spirits by telling her that they're "way better than Mulder and Scully." X-Files fans may not have taken kindly to the burn, no matter how subtle it was, but showrunner Michael Peterson has come out to explain what went into the decision to call out Mulder and Scully in the Bones finale:
As a longtime fan of The X-Files, I was happy to learn (thanks to Michael Peterson) that the mention of Mulder and Scully in the Bones series finale came from a place of love rather than derision. After all, the premise of Bones from the very beginning has had so many similarities to the foundation of The X-Files that it's hard to imagine Booth and Brennan ever would have made it to primetime if not for the success of Mulder and Scully.
Even as a longtime fan of The X-Files, I did appreciate the way Booth's final "Mulder and Scully" comment called back to a similar comment way back in the Bones pilot. When trying to convince Brennan that they'd be a great investigative team, he referred to them as "Scully and Mulder" in what was then a clear nod of respect to the show that arguably made so many series like Bones possible. The series finale comment did not come across quite as fondly, so it's a good thing the showrunner is on hand to clear things up.
That said, Michael Peterson and Co. put a lot of thought into how the comment would land with viewers. He went on in his chat with TVLine to say this about the X-Files mention:
All things considered, the Bones series finale was much more about tying up loose ends and providing closure than poking fun or creating stirs. If anything, the finale was a love letter to the fans, and given that there is apparently a lot of fan crossover between Bones and The X-Files, the Mulder/Scully comment was clearly not meant to offend. Besides, Booth's shoutout to The X-Files was one tiny moment in a pretty epic finale. There's just so much else to process.
Sadly, Bones has come to an end, and it's far too early to expect any news of a reunion. More X-Files might be in the works, however, so who knows? Maybe The X-Files Season 11 will have a shoutout to Bones. It's all one big Fox family, and stranger things have happened.