Ran's Father is riding the Shinkansen (Bullet Train) to Kyoto to attend a friend's wedding. Ran came along to see Kyoto, Conan came along because he's 'too young' to stay by himself, and the Detective Boys (including Ayumi-chan) were sent with Ran by their parents (traveling expenses paid, Ran points out).›
Conan suddenly encounters two men in black clothes.›He mistakes them for Gin and Vodka, the two who are responsible for shrinking him. However, they turn out to be similar, but not the same guys.›Using a gadget Dr. Agasa gave him, Conan listens to their conversation anyway (they were suspicious) and finds out they've given a boobytraped briefcase to someone who wanted illegal info on gold future prices. The two men get off the train, and Conan has less than an hour to find the case, before the whole train is destroyed in the explosion.
With the help (he didn't ask for it) of the Detective Boys, Conan narrows the suspects to four and then three people. However, he's made such a pest of himself that Ran drags him back to their seats. With less than ten minutes left, Conan starts to tell Ran who he really is, but at that moment, the rest of the case becomes clear. He pulls a trick to get away from Ran, and races back to the person with the bomb.
He's Too Late!!! The bomb has been activated and there's just ten seconds left till the whole Shinkansen is blown to Smithereens!
Using the muscle boosting shoes Dr. Agasa gave him, Conan kicks the bomb/briefcase through the glass in the nearby door window with only one second left! Whew. Everything gets cleaned up, even the two men who placed the bomb in the first place are caught in a police dragnet.
After the credits, Ran asks Conan what he was about to tell her so seriously, but the Detective Boys bail him out.