1. Angry Eyes

Cagalli, now Orb's head of state, and Athrun, now her bodyguard, are meeting with ZAFT's new head honcho, when 3 of ZAFT's newest mobile suits are stolen.

2. Those Who Call For War

Shinn continues to battle the three stolen suits. In the midst of the battle, the three machines work to escape from Armory-1 and rendevous with their ship, Earth's "Girtty Lue", which is under the command of the mysterious Neo Roanoake.

3. Warning Shots

4. Stardust Battlefield

5. Scars that Won't Heal

6. The End of the World

7. Land of Confusion

8. Junction

9. Bared Fangs

Eager for retaliation, the Atlantic Federation declares war on ZAFT (who they blame for the Junius-7 drop). In defense of the oncoming nuclear onslaught, ZAFT unleashes its newest weapon, the Neutron Stampeder, against the Atlantic Federation forces.

10. A Father's Spell

As Athrun meets with Durandal, the Durandal-endorsed psedo-Lacus, Meer Campbell, rallies the citizens of the PLANT's look away from war and look towards peace. Later, Durandal offers Athrun a chance to pilot one of ZAFT's newest mobile suits, the ZGMF-X23S Saviour.

11. The Chosen Path

12. Blood in the Water

13. Resurrected Wings

As the Minerva's crew congratulates Shinn on his job well done, Kira is forced to take the Freedom out into battle once again to take out the assassins that are after Lacus.

14. Flight to Tomorrow

15. Return to the Battlefield

16. Struggle in the Indian Ocean

The Minerva engages Neo and the 3 stolen Mobile Suits in a battle over the Indian Ocean.

17. The Soldier's Life

18. Attack the Lohengrin

19. The Hidden Truth

20. PAST

21. Wandering Eyes

An EA fleet led by Orb forces heads towards to Black Sea to deal a critical blow to ZAFT. However, a third party is waiting in the wings to stop the battle.

22. Sword of the Blue Skies

Cagalli's attempts to stop the Orb fleet fails and a battle between the Minerva, Orb/EA fleet and the Archangel breaks out

23. The Shadows of War

24. Differing Views

25. The Place of Sin

Shinn rushes an injured Stella aboard the Minerva. Once aboard, he learns startling information about Stella. Elsewhere, Lacus decides to go to the PLANTs and scope the situation out.

26. The Promise

27. Unfulfilled Feelings

All hell breaks loose in a three-way battle between the Minerva, Orb/Earth fleets, and the Archangel.

28. Survivors and Sacrifices

29. FATES

In order to save Stella's life, Shinn brings her back to Neo.

30. A Fleeting Dream

Shinn and Rey both receive pardons for freeing Stella, a Prisoner of War, much to Talia and Athrun's surprise. Meanwhile, a revitalized Stella pilots the EA's new heavy assault MS, the GFAS-X1 Destroy, and wipes out several villages on the Russian front.

31. The Endless Night

The Minerva and Archangel work to stop the Destroy and its destructive rampage through Europe. Shinn is shocked to learn that Stella is the pilot inside.

32. Stella

Shinn, swearing vengeance on the Freedom, studies up on it with hopes of defeating the MS that killed Stella. Meanwhile, the Earth Sphere is thrown into chaos as Durandal announces to the world that Logos is behind the war and this never-ending hatred.

33. The World Revealed

As the Archangel makes its way towards Orb, it is attacked by the Minerva. Having studied up on the Freedom, Shinn prepares to destroy it.

34. Nightmare

As the Archangel crew scrambles to stabilize their ship, Cagalli rescues an incapacitated Kira. Aboard the Minerva, Shinn gloats to Athrun about his victory. Dullindal decides to make his way toward Earth to present two new mobile suits to Athrun and Shinn...

35. Eve of Chaos

After his less-than-warm reception to Durandal, the Destiny and the Legend, Durandal decides that Athrun will only hinder his goals. With Special Ops soldiers after his life, Athrun decides to, once again, leave ZAFT.

36. Athrun on the Run

37. Thunder in the Dark

38. A New Flag

39. Kira of the Skies

40. Legacy of Gold

41. Refrain

42. Freedom and Justice

43. A Call for Counterattack

44. Lacus Times Two

45. Prelude to Revolution

46. The Song of Truth

47. Meer

48. To a New World

49. Rey

50. The Final Power

Kira in the Strike Freedom is confronted by Rey in the Legend. Meanwhile, Athrun in the Infinite Justice battles Lunamaria in the Impulse and Shinn in the Destiny. Requiem is destroyed in a joint effort of the Infinite Justice and Mu in the Akatsuki. The combined efforts of the Archangel and the Infinite Justice, damage the Minerva, causing it to crash onto the Moon. Durandal and Kira confront each other in the collapsing Messiah. Durandal is shot by Rey, and Captain Gladys orders Kira to leave as she, Rey and Durandal are killed when the Messiah falls to the Moon surface. The Second Bloody Valentine War ends.