This guide will show you how to get the Secret Ending in End of Abyss. To do this, you will have to find all 8 Data Shards. These are collectibles scattered around the map, usually in areas that you can only reach by finding keys or pressing switches. None of them are missable, and they can all be found after finishing the game. Once you have them all, take them to the Mainframe in Lower Levels > B3, then defeat the final boss again.
Do not pick up all 8 Data Shards before getting the normal ending: if you get the Secret Ending first, you will be locked out of the normal ending on that save, along with its trophy. Finish the main story first, then come back for the shards.
Here are the shard locations:
Data Shard #1
Lower Levels > F1.
You can reach it by burning down the wall in the hall to the north.
Data Shard #2
Habitation Sector > F1.
First, get the Security Guard Keycard by using an Explosive Charge on the wall just left of the Fast Travel Shuttle in the Containment Sector. Then use it to open the door on the right at the end of the corridor in the Habitation Sector. Head downstairs and through the door on the left to find the Security Chief Keycard. Use it to open the door on the left, back in the main hall outside. Then head through the door to the north to find the Data Shard.
Data Shard #3
Ventilation Tunnels > F3.
First, you must destroy the weak wall to the right of the easternmost entrance to the Tunnels from Factory East. You can do this with the Explosive Charges, which are obtained during the main story. On the other side of the wall, continue right until you eventually reach F2 of the Ventilation Tunnels. Here, head around the upper catwalk and pull down the ladder to reach F3. Then head all the way right and go up the stairs for an ambush encounter. After defeating the enemies, grab the Ventilation Maintenance Key.
Now use the key to open the door in the northern area of F3 to find the shard inside.
Data Shard #4
Factory West > F4.
First, you will need to get the Executive Level Access Keycard from the Outer Sector. To get there, use an Explosive Charge to blow a hole through the floor just outside the safe room in the Maintenance area. Then climb down and head all the way left until you see the key behind some boxes.
Now head to Factory West and use the key to access the lift on F2. Ride it up to find the shard in the second room with the large table.
Data Shard #5
Reactor > B1.
First, head to the room on the left of Waterworks > B3 and press the switch on the wall. You will need to have progressed far enough in the story to have the Grappling Hook.
After that, head to the right side of the circular structure near the top of B3 in the Waterworks and press the switch to drain some of the water.
Next, activate the pump by interacting with the console in the room on the eastern side of B3 to drain the water in that area.
Then head out through the door to the left of the pump console and climb down the ladder. Continue along this path and head north to the dead end. Here, use an Explosive Charge to destroy the wall and clear the blockage.
With that done, head through the door in the top right corner of B3 and follow this path to the end, where you will find the switch that drains the Reactor Pool. Along the way, you will have to open an Energy Node door and survive an ambush.
Now head to the Reactor Pool on B3 of the Reactor and climb down. At the bottom, take the path on the left and grab the Underbelly Key from the locker.
Finally, use it to open the door down the short set of stairs outside the Reactor, on the right side of F1. The Data Shard will be inside.
Data Shard #6
Waterworks > B3.
First, get the Sewer Workshop Key from the left side of the sewers area on B3. Then use it to open the small room at the bottom of the sewers.
Data Shard #7
Containment Sector > F3.
First, use an Explosive Charge to blow a hole through the wall on B1. Then look for a ladder you can pull down in the next room. Climb it and grab the Storage Room Key.
Use the key to open the door on F3, where you will find the Data Shard.
Data Shard #8
Lower Levels > B4.
Head down the stairs in front of the safe room on B3 to enter the Tunnels. At the halfway point, burn down the wall to find the Data Shard behind it.
Once you have all 8 Data Shards, take them back to the Mainframe on B3 of the Lower Levels.
Then defeat the final boss again to get the Secret Ending.