| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Arise, Serpentor, Arise! : Day 1 | 2 | 66 | Monday September 15, 1986 |
| Arise, Serpentor, Arise! : Day 2 | 2 | 67 | Tuesday September 16, 1986 |
| Arise, Serpentor, Arise! : Day 3 | 2 | 68 | Wednesday September 17, 1986 |
| Arise, Serpentor, Arise! : Day 4 | 2 | 69 | Thursday September 18, 1986 |
| Arise, Serpentor, Arise! : Day 5 | 2 | 70 | Friday September 19, 1986 |
| Last Hour to Doomsday | 2 | 71 | Thursday September 25, 1986 |
| Computer Complications | 2 | 72 | Friday September 26, 1986 |
| Sink the Montana | 2 | 73 | Monday September 29, 1986 |
| Let's Play Soldier | 2 | 74 | Tuesday September 30, 1986 |
| Once Upon a Joe | 2 | 75 | Wednesday October 1, 1986 |
| The Million Dollar Medic | 2 | 76 | Thursday October 2, 1986 |
| Cobrathon | 2 | 77 | Monday October 6, 1986 |
| The Rotten Egg | 2 | 78 | Tuesday October 7, 1986 |
| Glamour Girls | 2 | 79 | Wednesday October 8, 1986 |
| Iceberg Goes South | 2 | 80 | Thursday October 9, 1986 |
| The Spy Who Rooked Me | 2 | 81 | Monday October 13, 1986 |
| Grey Hairs and Growing Pains | 2 | 82 | Tuesday October 14, 1986 |
| My Brother's Keeper | 2 | 83 | Wednesday October 15, 1986 |
| My Favorite Things | 2 | 84 | Thursday October 16, 1986 |
| Raise the Flagg! | 2 | 85 | Monday October 20, 1986 |
| Ninja Holiday | 2 | 86 | Wednesday October 22, 1986 |
| G.I. Joe and the Golden Fleece | 2 | 87 | Monday October 27, 1986 |
| The Most Dangerous Thing in the World | 2 | 88 | Wednesday October 29, 1986 |
| Nightmare Assault | 2 | 89 | Thursday October 30, 1986 |
| Second Hand Emotions | 2 | 90 | Friday October 31, 1986 |
| Joe's Night Out | 2 | 91 | Monday November 10, 1986 |
| Not a Ghost of a Chance | 2 | 92 | Thursday November 13, 1986 |
| Sins of Our Fathers | 2 | 93 | Tuesday November 18, 1986 |
| In the Presence of Mine Enemies | 2 | 94 | Wednesday November 19, 1986 |
| Into Your Tent I Will Silently Creep | 2 | 95 | Thursday November 20, 1986 |
| G.I. Joe: The Movie | 2 | 96 | Thursday January 1, 1987 |