1. Shadowzone
2. Con Job (Character Debut/Death: Makeshift)
3. Crisscross (Character Debuts: Colonal Leland Bishop; in all)
4. Metal Attraction
5. Rock Bottom
6. Mini-Cons (Character Debuts: High Wire, Grindor, Sureshock and Perceptor)
7. Partners
8. T.M.I.
9. Stronger, Faster
10. One Shall Fall
11. One Shall Rise, Part 1 (Character Debuts: Unicron. Character Deaths: Tow-Line)
12. One Shall Rise, Part 2
13. One Shall Rise, Part 3
14. Orion Pax, Part 1 (Character Debut: Elita-1)
15. Orion Pax, Part 2
16. Orion Pax, Part 3
17. Operation Bumblebee, Part 1
18. Operation Bumblebee, Part 2
19. Loose Cannons (Character Debut: Dreadwing)
20. Crossfire (Character Debuts: Scavenger, Scrapper, Bonecrusher, Hightower, Long Haul and Devastator)
21. Nemesis Prime
22. Armada (Character Debuts/Deaths: Skywarp, Thundercracker, Ramjet and Thrust)
23. Flying Mind
24. Tunnel Vision
25. Triangulation
26. Triage
27. Toxicity (Character Debut: Hardshell)
28. Hurt (Character Death: Hardshell)
29. Out of the Past
30. New Recruit (Character Debut: Smokescreen)
31. Cylas
32. Twins (Character Debuts: Side Swipe and Sun Streaker)
33. Legacy
34. Alpha/Omega
35. Hard Knocks
36. Inside Job
37. Patch
38. Regeneration (Character Death: Dreadwing)
39. Darkest Hour (Character Deaths: Optimus Prime, Swindle, Scavenger, Scrapper, Bonecrusher, Hightower, Long Haul and Devastator
