As soon as you re-enter the simulation after rescuing Matt Miller, Kinzie will talk about some weird readings and a Warden will come crashing down. This Warden introduces the Stomp power, where it will jump up slightly and slam back to the ground, creating a shockwave that will knock you up into the air slightly unless you jump over it.
Fight the Warden like you have been doing all along, meaning to hit its shield with a power to drop it, then shoot it with your most powerful gun. Once it staggers, press the button that appears and finish the button mash mini-game to get a new power, Stomp. As usual, you’ll get some training with your new power and then the mission will be over.