Before we get started, I need you to know something important: I stopped watching Bones sometime around its fourth season. Despite this, I can say without any doubt that Season 2's "Aliens in a Spaceship" is the best episode of the entire Fox series. I don't need to have watched the final eight seasons of the Emily Deschanel and David Boreanaz crime procedural to know this to be true, because I have stared Bones greatness in the face, and it is that emotionally tumultuous but immensely satisfying episode, which brings home the life-or-death stakes of the characters' work by making it personal. Nothing else was ever going to top it, and nothing else ever did.
Bones fans already know what happens in "Aliens in a Spaceship," but I'm going to summarize it anyway. The episode begins in medias res, with Brennan (Deschanel) and an injured Hodgins (TJ Thyne) waking up in Brennan's car and realizing they have been buried alive by a serial killer known as the Gravedigger. From there the episode flashes back in time 48 hours, revealing the case of the week, which involves twin boys, also victims of the Gravedigger, who died after being kidnapped and trapped in what a local cop initially thinks is a spaceship (it's really a beer vat), hence the episode's title.
Once Brennan and Hodgins, who at this point in the series are colleagues but not yet close friends, have been kidnapped and buried alive, a ticking clock is attached to the proceedings — sometimes even a literal one, displayed on a screen in the lab as Booth (Boreanaz) and the Squints attempts to find them before their air supply runs out. This successfully ratchets up the tension to almost unbearable levels at times, something we rarely see on Bones since so much of Bones is about, well, bones and not warm, fleshy bodies that are running out of air.
The fact that Hodgins is also injured after being run over by the Gravedigger's car — he became collateral damage after interrupting Brennan's kidnapping, which parallels the case of the Kent twins — adds another layer of emotional turmoil to the story. Even if viewers feel relatively good about the likelihood that Booth and the rest of the Jeffersonian team will save their friends — no one is going to kill Bones off Bones, after all — the episode taps into our emotions by balancing the agonizing search for Brennan and Hodgins with the duo's intimate ordeal as they bond by confessing secrets to one another, discuss faith (or Brennan's lack thereof), and use their smarts to figure out where they are and how to send a signal to their coworkers, all while staring death in the face. The episode works so well on that level that it's surprisingly easy to ignore all logic and common sense and simply exist alongside the characters as precious time ticks by.
"Aliens in a Spaceship" is emotionally painful not just for Brennan and Hodgins — who, believing he might die, admits he's over the moon about Angela (Michaela Conlin). ("A man gives you a bottle of perfume like that ... it says 'I love you.'") The rest of the team is naturally also feeling unbearable strain as they attempt to beat the clock. Booth feels helpless after meeting dead end after dead end, and the pain radiates off him even before he starts angrily poking at screens and yelling about what Hodgins' cryptic text message means. After all, he and the rest of the team already know what happens to the Gravedigger's victims if a ransom isn't paid, and Booth isn't able to get the ransom together in time — because although Hodgins is the owner of the Cantilever Group, the third-largest privately owned corporation in the country, he also put into place a policy that prevents the company from paying a ransom if there's no proof of life.
It's a pretty convenient loophole that exists for no reason except to drive up the tension, but it ultimately doesn't matter. The story is emotionally engaging from every single angle, as everyone has something to lose, be it a partner, a romantic relationship, a friend, a coworker, or, perhaps most importantly, a future. And every member of the team has an important role to play in the proceedings, including Brennan and Hodgins, who use their brains to MacGyver themselves out of the situation as much as the team outside deciphers the clues. If just one member of the entire team is missing from the equation, Brennan and Hodgins' probability of survival diminishes.
The reason "Aliens in a Spaceship" really stands out isn't because there's a race against time or because Booth running to pull Brennan and Hodgins from the earth is such a memorable moment that it was later immortalized in the opening credits. It's because the hour places all of our beloved protagonists right in the middle of the action in a way we rarely get to see; Brennan and Hodgins effectively replace the bodies of the twin boys in the case. As a result, Bones was never more effective at telling a dramatic and personal story.
The episode also had lasting implications for the characters, furthering their relationships and propelling the narrative forward. After he and Brennan are rescued, Hodgins admits he can't sleep because he's afraid he'll wake up back underground, which leads to an invitation from Angela to stay with her, thus deepening their relationship. Meanwhile, Brennan's faith in Booth is confirmed, and the letter that she wrote to him while underground eventually reappears as her wedding vows in Season 9.
But the fact that the episode ends without the Squints actually catching the Gravedigger — the co-author of the book about the Gravedigger was initially supposed to be revealed as the culprit, though that later changed and the character wasn't unmasked until two seasons later — is an unsettling promise that there is still more to come. Bones is a series that relies on neatly solving cases. There's a particular pattern or rhythm to it. So when a case is left dangling wide open, especially one as personal and as emotionally involved as "Aliens in a Spaceship," it's bound to stand out as one of the best. This one certainly does, and that's a fact not even Temperance Brennan can argue with.
Bones is available to stream on Hulu.