Follow the mountain trail to quickly reach T-Bone's junkyard. There are a lot of militia personnel already there so use T-Bone's traps to eliminate them. After taking them all out, regroup with T-Bone. Follow and defend him from the incoming militia as he rig up the explosives to blow the place up. Use the traps he laid to make your job easier.
After he rigs up the second explosive, leave the junkyard through the back gate and take cover immediately. More militia will be waiting here, including a sniper on the far end. Use the traps and hack the nearby camera so you can remotely detonate the explosives the enemies are carrying. Take out the sniper then move forth to the tunnel nearby. Next, head to the boat and take T-Bone out of Pawnee. The game will take you automatically to the Bunker after a few moments. The mission will be complete after the scene.