A variety of the War Room scenes in Days of Ruin counts as this. They include Tabitha forcing Will to become her servant, Mr. Bear telling Penny to help Will, and Greyfield fleeing at the sight of Lin. Also, everyone, including Cyrus, telling Will to listen to the foe's advice on the Great Owl level.
Mission 4 has the Beast providing tactical advice. Much to Will's confusion.
The mission "Crash Landing" is a mostly serious (and often frustrating) affair, except for the generic enemy soldier's reactions to your tanks and rockets, and her attempts to get people to pay attention to the fact that the Great Owl is dropping. Eventually, she decides to get a parachute. Turns out, it's actually a sleeping bag. "...Ah, crap" is right.