Get out your silenced pistol and wait for the platform to reach the bottom. Walk up a ways then you MUST lay flat until the walking guard passes by. Crouch up the rest of the way but crawl past the open middle area over to the other side of the truck. Once behind the truck, crouch walk over to the doorway and get that locked picked as fast as you can. Sometimes the guard standing by the elevator will see you so quickly make sure that his back is turned before you pick the lock. Open the airshaft hatch, and close the door behind you. Run down the shaft and when you get near the opening at the bottom, crawl the rest of the way.
Lean upward and wait for the two patrolling guards to start walking away from you. Crawl out of the shaft and down to your left. If you crouch walk here, the guard at the bottom of the elevator will see you. Once behind the train, crouch walk over behind the boxes. Lean around and make sure that the patroling guard is walking away from you. Crouch walk behind the second set of boxes in front of the stairs leading to the control room. Crawl up the stairs. At the top, crouch over to the door, open the door, disable the computer AND MAKE SURE YOU PICK UP 3 GRENADES because you'll need them on the next mission.
Lean around the door and make sure that the patroling guard at the bottom of the stairs is walking away from you. Jump onto the railing at the top of the stairs and over the side. Crouch walk over to one of the lamp posts by the guard standing by the button by the big door. Lay flat and wait for the two patroling guards to start walking in the opposite direction. Shoot the guard standing by the big door in the head or break his neck. Active the door's control panel, then turn around and immediately run around to the opposite side of the train and jump into the first car.
Hit the train's button and then turn around and leap into the back railcar and keep going until you get into the last railcar. Lay down beside the barrels. If you lay down anywhere else on that train then the guards in the passing trains will see you. Remain hidden until the train comes to a rest. Alternatively, you can activate the train and then jump out of the train and RUN the rest of the distance to the end of the mission but it takes a while.
When the train stops, jump out of the train between the last two cars. Don't try to jump over the barrels because you'll find yourself stuck between the barrels and the side of the railcar and won't be able to move. Run over behind the shed. Open the airshaft door that leads to the Weather Station and go inside. Mission over.
If you do everything right, you can get through this mission without having been seen, 100% health, and on time.
I completed this in 4:57 without being seen, no damage, and 100% accuracy.