Open the door to free them, then approach the Mobile Command Center and use Smoke Shot to destroy the panels on either side. Near the Mobile Command Center, you'll find a cage which houses Conduit suspects. When all of the DUP forces are down, jump down to ground level and subdue anyone who isn't dead. If you're low on smoke, absorb some from the chimneys, and note that the chimneys respawn after a few minutes so you can keep recharging if you need to. Stay up on the roof and spend some time taking out the DUP forces below - it shouldn't be too difficult from your advantageous position, just keep ducking back if things get too hot. Head for the Mobile Command Center where two nearby buildings overlook it. You'll also find plenty of chimneys to recharge your smoke if you need to. Instead, find a nearby vent and head for the rooftops for a tactical advantage. You can approach from street level, but a frontal assault is challenging.
Your main objective from here is the Mobile Command Center, marked as the star with the square around it on the radar. This will help your Good Karma if you're going down that path. When everyone is down, check for enemies that you can subdue and civilians that you can heal. Don't waste your smoke if your target is too far away. Tip: If your crosshairs turn red while on an enemy, they are within range of Smoke Shot if they remain white, they are out of range. If none of the vehicles are smoking, shoot them and then replenish. If you run out of smoke, grab some from a nearby vehicle.
Smoke Shot only has a limited range, so use Smoke Dash to dart between the two-piece barricades and take out the DUP soldiers with Smoke Shot only when you're close. You'll now need to take out the DUP soldiers as quickly as you can. Things don't go according to plan, melee the closest enemy and quickly take cover. Run forward to the DUP checkpoint and have your hand scanned. This mission begins right after you save Reggie on the bridge in the previous mission.