The conclusion of the Season 6 finale sees the end of the gang's most incredible voyage.
The crew of the Nerius finds out that they were injected way off their mark from the brain and are in the foot. Archer tries to make tang with rubbing alcohol, but Lana and Slater reminds him that they have limited time to screw around. Slater tries to contact Agent Holly but finds that their communications are damaged. Holly finds Abbiejean is crying since she's hungry, but Malory still thinks she's too fat for a baby.
Archer wants to bail, but Slater and Dr. Sklodowska convince him otherwise. Archer suggests they use the laser to exit the foot to the outside, but Sklodowska reminds him that they're the size of bacteria. Sklodowska then suggests that they can laser through a blood vein, and travel in it to the clot. However, they'll be traveling 3 to 4 miles an hour, and being microscopic, they'll be traveling really fast. They reach the vein and laser cut it clean. Cyril reminds Ray that he'll need to talk to Lana about his racism over his robotic hand, but Ray says he was just upset over that he had a robotic hand, not about the color. Realizing the misinterpretation, Ray goes to talk with Lana, but when the ship reaches inside the vein, the speed up quickly and throws Ray across many steel bars crippling him into a quadriplegic. Sklodowska manages to direct Cyril through the veins, and they reach the blood clot. Before Archer can fire the laser, a white blood cell attacks them and plugs the turrets up. To make matters worse, TV's Micheal Gray stowed aboard, causing their oxygen levels to drop. The only way they can dislodge the blood clot now is for someone to swim inside the veins and use a portable laser to blast it. Archer volunteers and takes Pam along with him. With Pam's help, Archer manages to blast the white blood cells, and dislodge the blood clot.
Unfortunately, when they get back, Archer presses the decompression button which stalls the engines until it's all purged (which Archer comments it is a huge design flaw). After waiting a long time, they floor it to the tear ducts while the medical team use eye droppers to extract Kovak's tears, hoping one of them contains the Nerius. But even though they see a light, the Nerius expands, killing Kovak and the medical team. Malory tries to ask for another chance, but Holly stands by his word, firing the group from the CIA and blacklisting them from espionage. He also notes that even with Kovak's death, his work on Miniaturization is still in the database. However, Krieger at that moment destroys the servers in his rage, losing the data for Kovak's research. As Holly mourns the loss of both Kovak and his data, Malory mourns the end of her espionage career with nothing to show for it.
In the New Mexico desert, the group is trying to hitch a ride out, while battling the heat. Malory thinks that she could try and persuade Holly to get them back their jobs, but Lana says it's not really worth it especially since the CIA could have been trying to find excuses to fire them all this time. Archer agrees and notes that they never really belonged with the CIA, because they're the underdogs, the people who are looked down but always get the job done, raising the morale of the group. Malory reminds him that they still need money, but Archer puts on some sunglasses and says he might have a solution.
- Fantastic Voyage (1966): the premise of shrinking a manned craft to microscopic size in order to explore a human body is lifted from this classic 60s sci-fi movie.
- Bill Nye: When Dr. Sklodowska corrects Lana on the singular form of "bacteria," Lana responds with, "Thanks, Jill Nye."
- Ray is once again crippled, but unlike the previous season finales where it was usually due to Archer, it was his own fault. He got out of his seat just as the submarine began to accelerate.
- The gang is no longer working with the CIA, failing their latest mission.
- At the end Malory asks Archer what are they going to do for money, Archer puts on his sunglasses and replies that he has an idea. That idea is the formation of their private-eye business which is the basis for Season 7.
- "Krieger Out" is a reference to "Seacrest Out" a phrase used by actor Ryan Seacrest.
- This is the only season that Woodhouse does not make a physical appearance.
- Jackson Bostwick was an actor who starred in the first season of the TV series Shazam!, based on the DC comic's character. Bostwick played Captain Marvel, the superhero alter ego of Billy Batson, played by TV's Michael Gray.
- Sklodowska was the Polish maiden name of Marie Curie, a two-time Nobel Prize laureate.
- Slater: "So, I saw you coming on to Archer-- "
- Sklodowska: "Look, I'm a sexual being. If that is shocking to you, then so be it."
- Slater: "It's not, I was just gonna tell you he's had the clap so many times it's more like applause."
- Krieger: (smashes supercomputer) 'Krieger, out..." (drops wrench and walks away)