This is mostly a follow-instructions level. However, there's a couple tricky parts to it.
Watch out for that one run that is actually a garbage compactor in disguise (it will have a sludge-filled floor).
As the one term indicates, DON'T fire at the Jugger on the floor. Later, a task force will help you out with it.
In order to get the chip from the operating room, the only way up appears to be a grenade jump. Fortunately, a 2x recharger awaits to help you out with this jump. However, you can also get this chip on the *first* time through the level (that is, going through the trash compressor area) when you enter the hanger bay with the jugger. Head towards the Jugger, but avoid contact with any of the beings down there. There's a door at the end there, but its not accessible until you activate a switch that is facing the door on one of the columns in the hanger bay (to the left of the Jugger as you are facing away from the door.) Once you activate the platform and get through the door, you'll find yourself set upon by Devlins - clear these out, and you can get to the chip without a grenade jump.
When you return to the bay and the troops teleport in, sit back until either the enemy Jugger is destroyed, or the rest of the troops are taken care of. Then take over and finish it off, if necessary, from the safety of that overhead room.
When you are swimming in the sewage lines, you'll see a small niche where you can see a invincible power up and an oxygen recharger. The door to these is just back around the corner from it.
Also, at the end of this sewer system, there's an elevator that will lead you to a rocket launcher. This is located opposite the elevator to get to the top of the landing bay.