ATC stops the train - this is actually an important plot point in both "shinaksen explosion" movies:

https://en.wikipedia.org/wiki/The_Bullet_Train

https://en.wikipedia.org/wiki/Bullet_Train_Explosion

In the movies terrorists place a bomb on board and the train crew has to maintain a minimum speed or the bomb explodes (this is where that american movie with a bus got the idea). And they have to manipulate the ATC or else it will stop the train when they enter sections of the track with lower minimum speed, or else ATC stops the train and the bomb explodes.