See the following sub-pages for the lists of enemies in Trails through Daybreak II, sorted by location.
- Prologue
- Act I-B
- Dirke Memorial Park
- Condemned Sector
- Blacklight District
- Tyrell District Waterway
- Old Sewer System
- Seiden Waterworks
- Act II-A
- Taoyuan Restaurant
- The Eroded Cave
- The Great Spire
- Langport
- Heilong Cheng Zhai
- Act II-B
- Auber District - Abandoned Subway Line
- Coral Archipelago: Alternate
- Aramis Academy
- Aramis Underground Auditorium
- Underground Maintenance Tunnel
- Fragments
- Nemeth Island
- Nemeth Island - Ruins
- Nemeth Island Inlet
- Nemeth Island Cave
- Nemeth Island - Port
- Nemeth Island - Abandoned Village
- Nemeth Island - Lab
- EX: Nemeth Island - Cape
- Underground Cavern
- Windswept Canyon: Alternate
- Nemeth Island - Observation Deck
- Act III-A
- Condemned Sector
- Longlai Waterfall
- National Highways Suburbs
- Dirke Memorial Park
- Seiden District Waterway
- Act III-B
- Grand Circuit
- Dirke Memorial Park - Forest
- Submerged Terrace Another
- Act III-C
- Station Street - Underground Ruins
- Moonlight Vashtar Palace
- Underground Sewers
- Act III-D
- Metropolitan Expressway Tunnels
- Subway Maintenance Tracks
- Creil Hills at Dawn
- Tyrell District Waterway
- Act III-E
- Downtown Edith
- Orbal Network Corridors
- Republic Military Garrisons
- Presidential Office Entrance
- Act III-F
- Dirke Memorial Park - Entrance
- Hollow Gardens of Demise
- Finale
- Condemned Sector
- Oct-Radium
- Eighth Principle Observation
- EX: Märchen Garten
- Floor 10
- Floor 11
- Floor 12
- Floor 13
- Floor 14
- Floor 15
- Floor 16