Welcome to what appears to be Treacherous Mansion's Boss Mission, E-4 Ambush Maneuver.
And there actually is a Boo to catch here, but you'll get him automatically as part of the mission. To get started, use your Dark Light just right of the train car to reveal the engine itself, which will cause this mission's boss to appear. Despite initial appearances, you won't be just fighting one Boo, but multiple Boos that join together to form one giant one. So as you might have you're going to have to break him apart and attack each Boo individually. But to do this, you're going to have to have him run into the giant drill on the front of the train somehow. Fortunately, there's two main ways to do this, and it depends entirely on which attack the Boo decides to use. If the Boo dives underground, he's about to perform a charge attack in whatever direction you are. Position yourself near the front of the train, timing it so that the Boo runs right into the drill, busting him apart.
Alternatively, you can lure him run into any other part of the train to knock him out instead, nut now there's a second step. You'll now have to grab his tongue and aim him toward the front of the train--perform a charged attack to send him flying.
Now if the Boo decides to jump around instead, avoid him entirely three times to have him knock himself out. Then just launch him into the front of the train. Once the Boo is broken up into smaller ones, it's time to get to work. Like with the big one, you'll want to launch them in to the train, but this time you're aiming for the open cages being pulled by the engine. Now only one Boo can fit into each cage, so make sure you aim only for the open ones, as marked by the blue sign.
Oh, and when the Boos turn invisible on you, just use the Dark Light to reveal them. Now capture as many as you can before the Boos form back together into the larger one, then just repeat these steps until you've caged them all to complete the mission.
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