When Keiichi found his grandpa's diary and saw a treasure map inside, Skuld and Urd started to feel a great urge to search it. With the company of his friends, Keiichi arrives to Honda Inn, the place indicated on the map. Once the party is inside, they meet Honda Chieko, who seems to share a certain promise with Keiichi. Apart from all that confusion, it's time for Keiichi to have enough courage to say the words "I love you" to Belldandy.

Set in a different series of events, this story does not follow the previous Appleseed movie canon (despite being directed by the same director of the previous movies); it is an alternate story to their beginnings. Briareos is already a cyborg and did not become separated from Deunan to be later reunited in Olympus to join ESWAT.

Appleseed Alpha depicts the early days of Deunan Knute and Briareos in the 22nd century, as they embark on a journey throughout dystopic ruins of New York in search of the city of Olympus. They are hired by Two Horns, the warlord of the ruined city, to eliminate bipedal combat machines. During the fight, they encounter Iris and Olson, both on a mission. Deunan and Briareos befriend them and decide to join their mission.

Iris is tasked with preventing the malevolent cyborg Talos from capturing a secret weapon humans were building. Talos uses Iris to activate the gigantic war machine.

(Source: Wikipedia)

The unnamed main character has been having strange dreams, seeing strange things, and meeting strange people. He investigates these events and finds a strange girl named Aya. With her help, he discovers that his world may not in fact be real and many of the people he thinks he knows may not exist anymore.

The first episode is a summary of SM, SM R and SM S, the second episode is about Haruka and Michiru on a cruise ship. They fight one of the SuperS enemies and decide to leave this villain to the classical Sailor Team. (That's an explanation why the outer Sailor Team doesn't appear in this season.) In episode 3 Chibiusa uncovers one of her classmates as a monster and fights her with the Sailor Team in a vampire castle.