The mission to recover an alien POW.
Immediately, you're under attack by Sectoids. Kill a few, and they'll fall back to a high ledge. Pick them off.
Get up there and around the bus, and fight a few Outsiders, with a Shield Commander. The drop pod will release more Outsiders. Defeat this wave, and a Muton Elite will first jump on top of the tank then right next to the Drop Pod, so prepare any AoE attacks for when he lands. When he's done, a last wave of Outsiders will emerge.
Gather ammo and enter the bunker. Unlock the energy door on the left--- but before going through, head to the right side to get the Kinetic Acceleration schematics. Head through, and up the stairs, to an arena where some soldiers are facing off against a Sectopod and a drone. Take out the drone before it can heal the Sectopod, as a second Sectopod and a drop pod will soon drop right in the middle of the area, in the hole.
Open the traincar door, and you'll just see Mu'ut Jeen escaping. You cannot kill him here. He will Mind Control the agent on your left (in the Focus menu), and extract the location of XCOM's base from his mind. You must now hunt him down an execute him before he reconnects with Mosaic and exposes Site X to attack.
Pass through the pumpkin patch and the farmstead's basement, and up the yard; Mu'ut Jeen will show another abilty: self-duplication. He'll leave the shadow clone to fight you while he escapes. Again, he is unkillabe. The clone, however, is a big target.
Go through the barn, and into the Outsider fortification. Now you can freely attack him. In the meantime, a wide variety of Outsiders are in the area, as well as a Gunship appears overhead. It's a tough fight: keep moving, as Mu'ut Jeen and other Outsiders will regularly pepper you with grenades if you stay in that part of the map. There is a Rotary Plasma Cannon in the lower, more open hallway on the left.