The train station is quiet - good! The door out of it is blocked - bad!
There's not much to see here, but we know the aliens leave useful vents everywhere. Try finding one.
The facility is over to the right, so that should be your search area.
You might have to move something out of the way
You can move the minecart to the right to reveal it, but the air duct is secure.
After moving the minecart, use the wrench on it to crawl inside the facility hallway.
There's not much to do except use the wrench on another air duct to crawl inside the duct junction.
The duct junction lets you peer into many rooms - a crystal room reveals a huge vat of Substance X.
In the other facility, we combined Substance X, Substance F, and oil to make a plant grow huge.
A huge plant might be exactly what we need to stop the alien threat - let's get some Substance F!