Decoy (Pillage)
At a Neo UN development base, Yukie is being tested to pilot the Fafner Mark Nicht, however Idun, who has taken human form, assimilates Yukie and destroys the development facility. Kazuki, Maya, and Canon are unable to bring Kenji back to the Alvis base, following Mamoru's death. Soushi, still in the Siegfried System, faces his past. Kazuki, assisted by Tsubaki, tries to save Soushi. However, Idun suddenly attacks the island and attempts to assimilate the entire base. Though Maya, Michio, and Canon intercept, they are easily defeated. Michio then activates the self-destruction sequence and attempts to ejects, but he is captured and dies in the blast. Also, Soushi disappears, along with the Siegfried System, infuriating Kazuki.
Aired 12/12/2004EP 23 - Decoy (Pillage)

Fafner
Tatsumiyajima is the central island in the middle of a small cluster of islands, in a sleepy backwater of the Japanese isles. Not much happens there, and the island's young people go to school knowing that their lives are likely to remain peaceful and undisturbed. Or so they have been taught... but the truth is different. The fate of mankind is on the line, and Tatsumiyajima is the last line of defense against a hostile and incomprehensible enemy. At the center of it all, fighting for Humanity's continued existence, is the giant robot Fafner, the dragon that guards this final treasure of mankind.
(Source: Anime News Network)
Note: The last episode aired with a runtime of ~48 minutes as opposed to the standard 24 minute long episode. In the DVD release and subsequent home video releases of the series, the final episode was split into two separate ~24 minute long episodes.