The ship attempted to rescue Rocket, a crew member trapped in the Matrix while aboard the stranded Mariner, following a sentinel attack which killed all other crew members of the ship. Tragically, even after the Pequod had found Rocket and initiated the exit procedure, Agent Brown had, from inside the Matrix, found Rocket a few seconds quicker and killed him before he could be safely extracted.
The Pequod was later destroyed in a sentinel attack after venturing to the surface, far from Zion, in order to collect artifacts of pre-Machine War human history. The ship's captain, Flint, was the only survivor of the ship.
The name of the Pequod is a reference to the name of Ahab's ship in the novel Moby Dick. Hunters and Collectors borrows from the novel and even features a copy in the ruins of a surface city. Its relationship to the hovercraft, the Mariner, is a further reference to the novel.
The nameplate on the ship's core read:
MARK III № 9
MADE IN THE USA
This is an allusion to Mark 3:9, which reads:
- "And he spake unto his disciples, that a small ship should wait on him because of the multitude, lest they should throng him."
The biblical passage indicates a proposed exit Jesus could make to "rescue" him from the crowd; appropriate to the plot of There Are No Flowers in the Real World, in which the Pequod was sent to rescue Rocket, who was at risk from the Agents who were able to possess and attack as any of the bluepills in the Matrix at any given time.