As Trails in the Sky the 3rd does not have a quest system similar to other games in the series, the following is a list for the notebook entries corresponding to the main quest and Memory Doors.
| Section | Entry Name |
|---|---|
| Chapter 1: "Phantasma" | Investigation |
| Chapter 2: "The Otherworldly Capital" | Phantasma |
| Chapter 3: "Golden Road, Silver Road" | The Third Plane The Golden Road The Silver Road |
| Chapter 4: "The Dark Stigma" | The Fourth Plane |
| Chapter 5: "Labyrinth of Shadows and Light" | The Fifth Plane |
| Chapter 6: "The Guardians' Trials" | The Sixth Plane |
| Chapter 7: "The Distant Flames" | Aster House In Gehenna |
| Finale: "The Future We Dream Of" | Finding the Lord Phantasmagoria |
| Moon Doors | |
| Star Doors | |
| Sun Doors |
