Here you can take a shortcut and complete the level in an alternative way. Actually you take the advantage of a little bug and finish the level much quicker. What you gain is that you enter the Saucer Room only once (at the end) without needing any keys or passes and avoid all this backtracking again and again through the areas (moreover, you avoid completely the train area).

To follow this route, you do not need the Hanger Access Key (that the guard over the small missiles room drops), nor the first Code Clearance Disk (that you get from the guard in the yellow missile room) nor the Launch Code Pass (which you find on top of the Saucer). You will miss a few pick-ups and some kills, but note that some of the enemies will not be triggered and will not even appear if you follow this path.

First of all, you can go to the room with the small missiles and shoot the vent to get the 2nd Secret. Then go to the yellow missile room. Kill the guard at the opposite ledge, and if you want get his Disk, but if you follow this path, you will not need it anyway. Whether you take the Disk or not, however, you do not have to return to the small missiles room again, as long as you already found the Secret there and you do not need to kill the guard that holds the Hanger Access Key.

Climb down to the ground where the yellow missile is. Enter the passage and you will come across an opening on the floor. Jump to grab the ladder above it; climb down. Run down the corridor and flip the switch to open the door.

You enter a room with a glass-covered button and a receptacle (you were supposed to take a long route, locate the Saucer Room, get the Launch Code Pass and then return back here to put it in the receptacle, so as to uncover the button). Stand in front of the button, as close to the glass as possible. Roll on the spot. You should see Lara somehow behind the glass. Turn around on the spot and press Action. Lara will actually press the button behind the glass!!!

Immediately dash in the room at the back to avoid getting hit by the flames of the missile launching.

Get out of the room with the button, climb up the ladder and return to the hall where the missile was. Climb up the ladder to the right of the passage from where you just exited (the one leading to the ledge where the guard was). Now that the missile has launched, the trapdoor that blocked the ladder before is open. So, climb past the first ledge and dismount on the upper ledge and climb the next ladder. Dismount on the terrace and kill the guard. Go to the other end, flip the switch to open the door and enter the passage.

Get past the lasers and follow the passage to emerge in the yard with the watchtower. Kill the two guards and enter the room on the right to kill one more guard and grab the Code Clearance Disk he drops. Flip the switch and climb down through the trapdoor below the watchtower. Follow the passage with the moving laser and after the bend jump to grab the grate and climb down. Exit the open door, go left in the corridor and then go up the ramp that will lead you outside the Saucer Room. If you want to get a pickup, you can go right in the corridor and you will emerge in the train area. Go left and take the Shotgun Shells from beside the tracks, then return back in the corridor and follow the passage and the ramp to emerge outside the Saucer Room.

Pass carefully the green lasers (jump over the first two ones and crawl under the third) and enter the room behind the crates at the end of the corridor. Kill the guards and press the two buttons to open the timed doors and enter the room with the five switches. Flip the three (2nd, 4th and 5th from left to right) to open the door of the Saucer Room.

Get out and go to the Saucer Room. Now you have all that you need to complete your mission. You can use the Code Clearance Disk you already have (the one you took from the guard out in the yard) to open the doors, climb up to get the 3rd Secret, and finally enter the Saucer, get the artifact and end the level in one run. You can even get the Launch Code Pass from the top of the Saucer, but you will not use it, as you have already launched the missile ;-)