This guide will show you where to find all 7 Fast Travel Shuttles in End of Abyss. Once you activate them all, you will unlock the 
Shuttle Network Restored trophy.
None of them are missable, and they can all be found after finishing the main story.
Habitation Sector
Habitation Sector > B1.
You will activate this one automatically during the main story, after the first boss.
Factory East
Factory East > F2.
You will also activate this one automatically during the main story, after beating the first boss and riding the Habitation Sector Shuttle.
Factory West
Factory West > F2.
From the safe room in the middle of this floor, head left, then down, and open the Energy Node door.
Go through the Energy Node door and continue east along this path until you reach a room with a small set of stairs leading up to a door on your right. Here, destroy the boxes just before the stairs to reveal a small vent you can go through. Head through it, and once you come out of the second vent, ride the lift up.
Now head down the stairs in the bottom right corner to reach the Shuttle.
Waterworks
Waterworks > B2.
Head up the stairs on B3, just northeast of the circular structure.
Containment Sector
Containment Sector > F2.
This one is easy to get to. You will find it in the southeast corner of F2.
Reactor
Reactor > B1.
To reach this one, ride the large lift down from the left side of F3 in the Containment Sector, then head down the stairs to the south to find it.
Outer Sector
Outer Sector > B2.
Head to Maintenance > F2 and use an Explosive Charge on the floor just outside the safe room. This will blast a hole that you can jump down. From the room below, head left and continue along this path until you reach the Outer Sector's Shuttle.
