Runaway Locomon is the second movie of Digimon Tamers, set after the final episode.
A train with a face shines in the darkness.
Rika is at the train station talking on the phone to Takato, who says he wanted what he was planning to be a surprise. Rika says she hates surprises. Guilmon jumps out of a box, which Takato has him hiding in for reasons unknown. The strange train suddenly rides across the railroad, and Rika runs off.
A report is broadcast about the runaway train, which is actually a Digimon named Locomon.
As Jeri, Mrs. Katou, and Calumon are decorating a cake, they see the report, where people try to figure out who is operating the train and how to stop it before it can cause any damage. MarineAngemon watches the report at the train station while Kenta carries a stack of boxes. Locomon goes by Kazu and Guardromon, who run after him.
As Locomon nearly hits the train Henry is on, Takato and Guilmon rush to face Locomon. Guilmon digivolves to Growlmon and stops Locomon's path with his arms. Locomon says "I wanna run! I wanna keep on running!" He powers up and knocks Growlmon off the bridge. Takato jumps on Locomon and tells Growlmon to tell Henry what's going on and to tell him to get the others.
Henry's train stops at the train station, where some of the train services are suspended due to Locomon.
Takato enters Locomon, whose insides are identical to a real train, and heads over to the engine room.
Meanwhile Rika races toward Locomon, and Renamon appears alongside her.
Henry, Terriermon, Suzie, and Lopmon notice a dark cloud with red in the center: A digital zone.
As scientists watch the train grids on computers, Yamaki appears, taking charge of the operation. He says that by looping around the city at a great speed, he created a spacial warp within the digital zone.
Kazu and Guardromon meet up with Kenta and MarineAngemon, and later Guilmon, who tells them that Takato is on Locomon.
Takato finds Locomon's engine room, but can't find anything that resembles a brake. Rika and Renamon jump onto the coal car and enter the engine room. Rika uses a Shellmon card on Renamon, who uses Hydro Blaster on the engine, but the heat causes the water to evaporate. The surprise Jeri was planning for Rika is revealed to be her birthday. Beelzemon rides by on his new motorcycle, and shoots Locomon's wheels with Double Impact, to no effect. Locomon uses Wheel Grinder, smashing Beelzemon's motorcycle and sending him flying.
Guilmon, Kazu, Guardromon, Kenta, and MarineAngemon meet up with Henry and Lopmon, who accidentally switched places with Terriermon, who is currently with Suzie.
On Yamaki's orders, workers modify the track manually to switch it. One of them notices Takato and Rika on the train and contacts the scientists, who tell Yamaki. Yamaki calls Rika's cell phone to talk to Takato, telling him of his plan and that they should get off Locomon as soon as possible. Rika doesn't trust Yamaki or want his help.
Kazu, Kenta, Henry, Lopmon, and MarineAngemon get on a small gold train which Guardromon pushes to chase Locomon while Guilmon digs a hole.
While picking up a wrench in the engine room, Rika is possessed by something with tentacles. At first she sings a song, and then she attacks Takato and Renamon with the wrench. Guilmon comes out of the hole he dug as Locomon goes by, and grabs onto the edge of the railing with his tail. When Henry and the others reach Suzie and Terriermon, Terriermon and Lopmon switch back to their original tamers. Guilmon gets on board Locomon, when Rika knocks Renamon out the window, and Guardromon catches her. A purple laser blasts the roof of the car they are in, where Guilmon is.
Guilmon uses Pyro Sphere on part of the wall of the train, revealing some spiderlike tentacles. More tentacles appear on Rika's back, part of a parasite called Parasimon, who is possessing Rika. His brother, considered the Parasimon leader, was possessing Locomon all along. Parasimon Rika shoots energy waves at Takato, which knocks him off the train and he hangs onto the edge. Guilmon uses Rock Breaker to destroy the Parasimon possessing Rika. When Locomon reaches a certain point, a worker hits the switch to change the path, sending Locomon down a new track.
Guilmon gets Takato back on top of Locomon, but as he turns, Rika, who is unconscious, nearly falls off, waking up at this exact point. Takato takes her hand to keep her from falling. Locomon digivolves to GranLocomon, his Mega form. Renamon gets Rika back inside GrandLocomon, before Parasimon tries to possess Rika, wrapping his tentacles around her. Takato and Guilmon biomerge to Gallantmon and sever his tentacles. Takato says Parasimon was possessing Rika and Locomon. Renamon says thanks to him, they got to hear a beautiful song. Parasimon says Locomon will run forever, and shoots a laser from his mouth at the digital zone, saying "Come on down!"
Multiple Parasimon begin to bio-emerge from the digital zone. Parasimon's plan all along was to control Locomon to create the digital zone so that he and his army could invade Earth. Henry and Rika biomerge with Terriermon and Renamon into MegaGargomon and Sakuyamon, and they and Gallantmon destroy several Parasimon. Justimon appears, and he, Guardromon, MarineAngemon, and Beelzemon destroy more Parasimon, but there are too many for them to handle at once. When Sakuyamon and Justimon are nearly possessed by some Parasimon, Takato's determination not to let Parasimon win transforms Gallantmon into Crimson Mode, who flies into the digital zone and destroys it with Crimson Light, sending a wave through Shinjuku that destroys all the Parasimon. Now free of Parasimon's control, Locomon goes through the portal to the digital world.
At Rika's house, Takato, Guilmon, Henry, Terriermon, Rika, Renamon, Jeri, Calumon, Kazu, Guardromon, Kenta, MarineAngemon, Ryo, Cyberdramon, Suzie, Lopmon, and Impmon celebrate Rika's birthday. After Suzie finishes singing a song, she says it's Rika's turn, and Kazu says Rika sings like a bird. Takato told Kazu not to mention that, and Rika walks away. As Rika's mother begins singing, Takato and Renamon walk down the hall while Rika watches the sunset, singing the first line of the song in her head.
- With the exception of Lopmon/Antylamon, all of the tamers' Digimon fight against an invading army, so that they are all in action at the same time, and in the end the enemy is destroyed when the main character destroys their base. This is similar to the battle with the Chitauri in The Avengers, except that the Chitauri leader, The Other, survives their destruction.
- It is unclear why Takato is making Guilmon hide in a box when Dolphin made the world aware that the tamers' Digimon were not evil monsters like Vikaralamon. It could be that people not living in Shinjuku (as would often be seen at a train station) aren't used to Digimon yet, or that Takato wanted to keep a low profile for the sake of Rika's surprise party.
- This is the fourth (possibly third) time blood is shown, first three being with Mihiramon, Gallantmon, and the D-Reaper. In this case Parasimon's blood is shown, both the leader when his tentacles are severed, and the minions when some of them are killed.