Single mom Natalie Teeger hears a noise in the middle of the night. She checks on her daughter, Julie, and then goes to her living room. An intruder lunges at her out of the darkness, and a vicious struggle ensues. In desperation, Natalie grabs a scissors and stabs the intruder, killing him.
Captain Stottlemeyer and Lieutenant Disher arrive to investigate the case. It turns out Natalie had another intruder in her house a couple of days earlier: a man posing as a water meter reader who looked around her living room and took off. Nobody can figure out what the crooks were after, so Captain Stottlemeyer recommends that Natalie contact Monk.
Monk is still reeling from the loss of Sharona, who has remarried her ex-husband and moved back to New Jersey, but he agrees to take Natalie's case. At her house, he finds a fish net that the intruder left behind, and theorizes that the crook must have been after young Julie's pet fish. But why? There's nothing extraordinary about the fish. The only clue the police have is a note they picked up on the deceased intruder that reads: "2:30 ¿ Sea of Tranquility." Natalie knows what it means: it's an exhibit at the local science museum about the Apollo moon landing. Her daughter Julie had been there the previous week on a school field trip.
Monk and Natalie go to the science museum to investigate. While there, Natalie recognizes a tour guide as the first intruder to her home. They lose track of the tour guide, but Monk is now focused on the science museum.
Back at Natalie's house, they find an aquarium kit that Julie had purchased at the museum the week before. Monk suspects that the thieves have hidden something in the kit that they want back. Monk wants to do an analysis of Julie's aquarium, but he has to wait: Julie has a science fair at school, and the aquarium is her project.
On their way to the science fair, Monk has an epiphany. He calls Stottlemeyer: the thieves were after a valuable moon rock they had stolen from the museum and hid in Julie's aquarium kit! At the science fair, Julie is presenting her aquarium, when the tour guide from the museum appears. He goes to Julie's aquarium and scoops out the moon rock - but he also takes Julie's pet fish! Monk chases the thief, who eventually falls and drops both the moon rock and the fish. Monk decides to save the fish first, with Stottlemeyer arriving just in time to prevent the thief from making off with the moon rock.
Natalie saw Monk save the fish, and was moved by his decision to put Julie's pet ahead of the valuable moon rock. Tired of her job as a bartender, Natalie decides to accept an offer to become Monk's new assistant. Monk has cracked another case, and, in the process, gained a new assistant to help him solve San Francisco's most baffling crimes.