The Doctor and Peri land in desolate ruins on Earth, tens of thousands of years in Peri's future. The Earth had been attacked by the Pararachnids, huge space-borne swarming aliens who left the planet in ruins and incidentally left several colonies of Pararachnids behind. The humans that survived the attack built tunnels underground and set up the Line, a place where they were put in a kind of suspended animation and were fed and exercised by robots called Monitors. The Doctor came to this time to find an item he needs to recalibrate the TARDIS.
A young man named Kimo Ani is awoken by a talisman. It tells him to leave the tunnels and head for the surface of the Earth. He manages to sneak by the Monitors. On the surface, he meets the Doctor and Peri. He runs away, and the Doctor and Peri give chase. When they catch up with him, he throws the talisman at them. The Doctor approaches Kimo Ani and talks with him. Peri picks up the talisman, which talks to her. It is a spaceship of something like intelligent bacteria who call themselves the Wibliwee.
Suddenly, a Pararachnid appears. The Doctor protects Kimo Ani and orders Peri to return to the TARDIS. The Doctor surrenders to the Pararachnid. Peri, meanwhile, is caught by two Monitors, who are searching for the missing Kimo Ani. When they threaten to destroy her as a hostile, she surrenders to them and they take her underground.
The Doctor and Kimo Ani are taken to the Pararachnid village, and sent to be prepared as a meal for the Breeder Male. The Doctor convinces the Pararachnid chef to let him go so he can advise it on the best spices to use on himself and Kimo Ani. He finds the cayenne pepper and blinds the chef with it, and he and Kimo Ani make their escape.
Meanwhile, the Wibliwee explain their plight to Peri. They've been stranded on Earth for years. They are without power, and they just happen to use a six-dimensional anomaly for their navigation, which is the item the Doctor was looking for. The Monitors put Peri into the Line in Kimo Ani's place.
The Doctor and Kimo Ani make it to the TARDIS and rematerialise in the Line. The Doctor finds the Wibliwee, who tell him where Peri is. Suddenly a swarm of Pararachnids break into the line and begin feasting on the unconscious humans. The Doctor and Kimo Ani retreat to the control room, staffed by a man who died some time ago, leaving the Line to run automatically. The Doctor has Kimo Ani stop the Line, which brings the Monitors. The Monitors attack the Pararachnids, destroying them.
The Doctor and Peri, after a mutual exchange of help with the Wibliwee, leave Kimo Ani and the surviving humans to rebuild the Earth.
- The Pararachnids swarmed on Earth, leaving it mostly in ruins.
- The Wibliwee became stranded on Earth after losing their nuclear core.
- Peri becomes upset when she sees that the Pararachnids left huge markings (like graffiti) on the Moon.
- Peri refers to Time Lords, World Meddlers, Eternal Guardians, Spectres, Ghouls and prehistoric gods which exist outside of 4D Minkowski space.
- The Doctor refers to the gnab gib, also called the big crunch.
- Moon Graffiti was originally an audio story included in the anthology Out of the Darkness. It was adapted into a prose story for More Short Trips.
- Kimo Ani previously appeared in PROSE: The Mary-Sue Extrusion.
- When the Doctor searches through a little notebook to find information about his item, he finds, among other things, a reference to the Hand of Omega. (TV: Remembrance of the Daleks)
- The Doctor says he damaged the TARDIS in his post-regenerative state (TV: The Twin Dilemma) and requiring Zeiton-7 was only one of the problems. (TV: Vengeance on Varos)
- The Doctor asks Peri how much she knows about the cosmology of Event One. (TV: Castrovalva, Terminus, AUDIO: Slipback)
- The Doctor mentions a version of him that was fond of making fun of himself with a penny whistle. (TV: The Power of the Daleks et al)
- The Doctor says he learned escapology from Houdini. He has made this assertion on several occasions (TV: Planet of the Spiders et al)