| Title | Season | Episode # | First Aired |
|---|---|---|---|
| The Five Faces of Darkness (1) | 3 | 66 | Monday September 15, 1986 |
| The Five Faces of Darkness (2) | 3 | 67 | Tuesday September 16, 1986 |
| The Five Faces of Darkness (3) | 3 | 68 | Wednesday September 17, 1986 |
| The Five Faces of Darkness (4) | 3 | 69 | Thursday September 18, 1986 |
| The Five Faces of Darkness (5) | 3 | 70 | Friday September 19, 1986 |
| The Killing Jar | 3 | 71 | Monday September 29, 1986 |
| Chaos | 3 | 72 | Tuesday September 30, 1986 |
| Dark Awakening | 3 | 73 | Wednesday October 1, 1986 |
| Starscream's Ghost | 3 | 74 | Thursday October 2, 1986 |
| Thief in the Night | 3 | 75 | Monday October 6, 1986 |
| Forever Is a Long Time Coming | 3 | 76 | Wednesday October 8, 1986 |
| Surprise Party | 3 | 77 | Thursday October 9, 1986 |
| Madman's Paradise | 3 | 78 | Monday October 13, 1986 |
| Carnage in C-Minor | 3 | 79 | Tuesday October 14, 1986 |
| Fight or Flee | 3 | 80 | Wednesday October 15, 1986 |
| Webworld | 3 | 81 | Monday October 20, 1986 |
| Ghost in the Machine | 3 | 82 | Tuesday October 21, 1986 |
| The Dweller in the Depths | 3 | 83 | Thursday October 30, 1986 |
| Nightmare Planet | 3 | 84 | Friday October 31, 1986 |
| The Ultimate Weapon | 3 | 85 | Monday November 10, 1986 |
| The Quintesson Journal | 3 | 86 | Tuesday November 11, 1986 |
| The Big Broadcast of 2006 | 3 | 87 | Wednesday November 12, 1986 |
| Only Human | 3 | 88 | Thursday November 13, 1986 |
| Grimlock's New Brain | 3 | 89 | Friday November 14, 1986 |
| Money Is Everything | 3 | 90 | Monday November 17, 1986 |
| Call of the Primitives | 3 | 91 | Tuesday November 18, 1986 |
| The Burden Hardest to Bear | 3 | 92 | Wednesday November 19, 1986 |
| The Face of Nijika | 3 | 93 | Thursday November 20, 1986 |
| The Return of Optimus Prime (1) | 3 | 94 | Tuesday February 24, 1987 |
| The Return of Optimus Prime (2) | 3 | 95 | Tuesday March 3, 1987 |