Chapters (50)
- Episode 50 - The Vessel of Mystery (Series Finale)
- Episode 49 - Ayeka
- Episode 48 - The Father
- Episode 47 - Over and Out
- Episode 46 - The Murasame
- Episode 45 - Captain 103
- Episode 44 - The Gun
- Episode 43 - 002
- Episode 42 - The Revenant
- Episode 41 - The White Whale
- Episode 40 - The Baby
- Episode 39 - The Young Hurricane
- Episode 38 - The Grandfather
- Episode 37 - The Traitor
- Episode 36 - Dinosaurs
- Episode 35 - Red to Black
- Episode 34 - The Orphans
- Episode 33 - Undone
- Episode 32 - The Bell Tower
- Episode 31 - The Monster on the Roof
- Episode 30 - The Daughter
- Episode 29 - Two Wrongs Do Make a Right
- Episode 28 - The Messenger
- Episode 27 - The "Lesson"
- Episode 26 - Wargames
- Episode 25 - Echoes from the Past
- Episode 24 - The Ronin
- Episode 23 - Nicer or Faster
- Episode 22 - The Time They Stole
- Episode 21 - Big Fish
- Episode 20 - The Astorian
- Episode 19 - Friends of Mystery
- Episode 18 - Our Mission
- Episode 17 - One Shot
- Episode 16 - The Spider in the Pond
- Episode 15 - The Monastery
- Episode 14 - Under the Cherry Tree
- Episode 13 - The Scientist
- Episode 12 - Together
- Episode 11 - Trick or Treat
- Episode 10 - A Great Team
- Episode 9 - The Protector
- Episode 8 - Unforgiven
- Episode 7 - The Trial
- Episode 6 - Hit, but Not Sunk
- Episode 5 - Game Over
- Episode 4 - The Rider
- Episode 3 - The Black Compass Project
- Episode 2 - The Deep Garden
- Episode 1 - Agent 103