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After the base, Jock flies drops you down in a junkyard, just beside an empty gas station where Savage's daughter is being held. You'll be near a locked door, but we can get the key by walking straight ahead a ways to the three people standing around the campfire. One of them is Sandra Renton from Hell's Kitchen, NY, apparently on her way to Eugene, OR. Another one will sell you supplies and give you a key to enter the door. Alternatively you can get the key just beyond the campfire by searching through the wreckage.
Head back to the locked door, use your nanokey, and climb up the ladder to emerge in a small fenced in area with a hole in the fence. An MJ12 guard patrols nearby, and to the right of the guard, MJ12 commandos are not far off. Note that if you alarm the station, Tiffany Savage will be shot and your mission failed, so don't cause any ruckus until you're sure she's safe.
Sneak out the hole and prod the trooper. Beware the MJ12 commandos to your right and head to the hill on the left side of the station. Climb up, stay crouched and crawl behind the gas station where you'll see a guard near a ladder, and beyond him, a couple dobermans. Carefully drop onto the top of the fence behind the gas station, sneak behind the guard and prod him unconscious. Climb the ladder and drop into the station from the roof of the building.
Search for supplies, and head back outside and around to the hill when its clear, drop down behind the station, climb the ladder and this time silently jump onto the roof of the next building. It's where Tiffany is being held. Drop down into the room from the roof and crouch. Get a gas grenade ready and toss it into the room where an MIB and MJ12 trooper await. Take them down as they cough, and when its done, open the nearby door to rescue Tiffany. Tell her to stay put until the commandos outside are taken care of. Now do your thing. You can use your prod on their lower back when they're not alarmed, as explained before, or take them out however you choose.
When its clear outside, tell Tiffany to make a run for the chopper. Meanwhile you can climb in the tank trailer for some extra supplies, and break into the nearby shed through the side window (by using a crate) for a repair bot and supplies.
When ready, Jock will take you to the Ocean Lab.