Bowser Jr.'s Boomsday Machine is the first mission of Bowser Jr.'s Boom Bunker. It is available when the galaxy is unlocked.
Upon landing, Mario will find that he has landed in the Megahammer's Junkyard. He needs to get a Bullet Bill on his trail and lure the bullet bill to a glass tank. If he is successful, Mario can use the cannon to go to the next planet. If he hits the target's bull's eye, Mario will get a 1-UP.
On the Cannon Planet, Mario must time his launch to get to the Spinning Platforms Planet. Landing on the target's bulls eye will net a 1-UP, but the target's angle means that the bulls eye is harder to hit. Mario must navigate the spinning platforms to make his way to the top. The northern segment requires his cloud form, and at the north is a stack of stone wheels. Upon their destruction, the wheels reveal another Launch Star, which leads to the boss area.
After making his way to the boss area, Mario confronts Bowser Jr. for the last time. Bowser Jr. shows off his now Boomsday Machine. After it is activated, it begins attacking Mario. A Fire Bar rotates around the tank's base Mario needs to use his cloud form to create a series of platforms that lead to the tank's weak spot: the cage at the top. However, staying up there is not recommended, so use your Ground Pound quickly, lets Mario will be sent flying off and get hurt. After its cage takes a hit, the Boomsday Machine gains a new attack: a vacuum that sucks in the clouds. The clouds will reform in their place eventually, but touching the machine's body causes damage to whoever is audacious enough to do so.
After it gets ground-pounded again, the Boomsday Machine doubles in size, sprouts treads, and can move. Now its vacuum breath can reach the highest clouds, and it can change its position to throw Mario off. The fire bar After it is hit one last time, it is destroyed, Bowser Jr. is sent flying to his doom, and a Grand Star appears so Mario can finish his mission.
- When Mario hits their bulls-eye as he is flying from the Cannon, the targets can change their colour from red to blue in the case of the first target and yellow in the case of the second target.