First, complete all stories from Stage 1 through Stage 4 in order, engage in conversations with key NPCs, collect items, and strengthen yourself.
You can check your progress by viewing the Journal (J key). If your conversation with the NPC has advanced, all entries except the bottom one should be filled up to “III”.

The first ending you'll see is Ending C. This ending is a unique bad ending, but if you want to see all the endings, it's the one you'll see first.

Once you reach Stage 5, just play normally until you reach the final boss.
Don't forget to talk to Nadia. She's at the entrance in 5-1, in the room near the elevator in 5-2, and in the computer room in 5-3.
After defeating the boss in 5-3, a special cutscene will play and the gate will open. Save your progress immediately after talking with the injured Nadia, and under no circumstances save again afterward.

Enter the gate and converse with the mysterious entity. When choosing the sacrifice, select yellow.

After that, collect the Rune, return to the Hub Level, and climb the Dark Tower without saving. Encountering Avlan will trigger Ending C.

If you regret seeing Ending C, load your save file from after defeating the final boss in Chapter 5-3.
To prevent the tragedy from repeating, choose a sacrifice other than yellow. For example, green.
From here on, you can save as many times as you like.

Then... retrieve the Rune, climb the Dark Tower, and encounter Avlan.
Approach him without attacking to trigger Ending B.

If you are not satisfied after seeing Ending B, you must achieve your original objective.
Melt down unwanted weapons, enhance the ones you need, cover your beloved plushie in buttons, and become as strong as possible.

After completing the enhancement, climb the Dark Tower once more to encounter Avlan. Shooting him will trigger Ending A.

You've come this far, and you won't be satisfied with the result. It's time to go break the curse.
To complete Nadia's event, first talk to Nadia at the hub level. Then head to 5-1, where you'll encounter her again a short distance past the starting point.

With Nadia lifting your curse, all NPC events have concluded, opening the path to the TRUE PACIFIST route. Climb back up to the Dark Tower, shoot Avlan as he reaches out his hand, and keep firing bullets until the old man stops moving.

When Avlan is defeated, Ending D begins.

If you are not interested in Ending C, you can choose to clear all of Stage 5 first. In this case, advancing Nadia's NPC event will lift the Yellow Curse, preventing you from seeing Ending C.

However, you will be able to fight Avlan on Route A without suffering the effects of the sacrifice.