The PlayStation 3 and Vita versions of this mission are related to a trophy named "Bombs on a Train", completing this mission will reward you with a bronze trophy.
The bomb train here will go down the track at a steady pace, with the timer noting down when it's about to crash. The only way it can crash is if it hits a closed (for the cart, from your position they are opened) piece of the track. To open the track up for the train (again, for you it looks as if you close it) you have to shoot the red light below the raised piece of track.
Move down the path, using the JET-Board if needed while using the Blaster or Beam Reflexor whenever you come upon another closed section of the track. You will encounter more manta and gekko enemies but they won't pose a challenge.
Head through the newly opened door to start the next mission; "Defeat Veger's Precursor robot".