There are three endings, decided by the final choice and the Lily gauge. Story details are left out.
Endings
Return to the Colony: decline the final offer.
Cost of Lost Memories: accept, with the Lily gauge below 100%.
Making New Memories (secret): accept, with the Lily gauge at 100% before Spire 4.
The gauge rises from Lily-related documents and data (some guides say side quests count too).
Two points of no return: the Orbit Elevator after the Great Desert, and the Nest after Spire 4. Make a manual save before each and you can see all three endings in one playthrough.
Epilogues
Patch 1.4.1 (September 2025) added an epilogue for each ending and a hidden request on the board.
New Game+
Unlocks after any ending.
Carries over: items, gold, gear, skills and SP, suits, cans, Data Bank.
Resets: main and side missions.
New: 34 Nano Suits, 5 accessories, new Beta moves and upgrades, drone skills, and the Raven Suit right away.
Easy-to-miss trophies
Naytiba Researcher (67 types): the Cocoon Naytiba appears only in Eidos 9 before Orcal's Testimony.
Meticulous Explorer: open nearly every camp (87/89) before the final area.
Lonely Fisherman: catch 20 fish. Can Collector: all 49 cans before the points of no return.
Unlock Ambush, Perfect Dodge and Focus Boost early for the related trophies.
Based on the Fextralife wiki and the PowerPyx trophy guide.