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Revisiting the Capsule "Ellie before" you'll notice that the dialogue has changed a bit. She now gives you the "coordinates" of her "library" which you then can access over the capsule on the right. In here you find some more lore snippets (which also build another connection to 20XX lore) as well as the 4 clues that you need to solve in order to progress through the rest of the hidden story.

The Void - Don't pick up any Core, Weapons or Powers. Clear Stage 8
Core Genesis - Collect 50 Scraps, then enter Dustria Stage
Clear Stage 9 of Boss Rush. (Not shown in this video, but i can if anyone wants to see that).
His Home - Pick up 3 or more Prototype Augmentions from the Very safe lab, then enter the Burning Temple Stage.

Once you've done the prior ones and these, the center Capsule will appear, leading you to the "Scripture" stage. This one is pretty difficult when done blind so you might need a few attempts on it. Once you've cleared it, you obtain the final piece you need to unlock the path to the true ending.

I might do a seperate video of the true ending.