On Archer Season 6 Episode 13, part two of the season finale, Archer and the gang continue where they left off, attempting to navigate their way through Dr Kovacs' body. After some trouble communicating with the control room, they finally realize that they're in Dr Kovacs' foot, and make their way into the body's circulatory system.
However, while entering the blood stream, Cyril decides to tell Ray at that moment that his actions and remarks about his hand sounded racist. Ray, horrified that he came across that way while he was actually just upset about his hand being robotic, tries to go apologize to Lana. As he gets up, the force of the bloodstream jolts the ship, and Ray ends up paralyzed at the back of the ship.
Cyril takes the pilot position, and manages to steer the ship to the arteries in the brain. Slater realizes that the ship is running out of oxygen because they have a stowaway; TV's Michael Grey is on board. To complicate matters further, the ship gets attacked by leukocytes which block the lasers.
Archer and Pam leave the ship to fight the phagocytic leukocytes and lyse the thrombus, and the ship continues on to their extraction point in the tear duct. Unfortunately, they get there a couple seconds too late, and the ship goes back to normal size while still inside Kovacs, killing him.
Hawley officially blacklists the gang from espionage work for the CIA, but not before Krieger destroys the computer that has all of Kovacs' work. Ray dies from sepsis from his injuries on the ship (and inflicted by Cheryl), while the gang attempts to hitchhike. Malory despairs about what they will do in the future, but Archer, relishing their status as underdogs, says he has a plan.