My guess on what is happening:
Mario and Luigi are going into a meeting with the big shots of the Mushroom Kingdom (This happened after the virus went through the Mushroom Kingdom causing Toads to implode). Luigi falls asleep, because he thinks he won't be asked about anything. Toadsworth, unknown named yellow bomb, Peach and Mario try to find a way to fix the Toads. Bowser comes in and crashes the meeting. And thats that. My guess is that shortly there after, they get swallowed by Bowser.