Soukyuu no 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.