The Layzner OVA serves as an alternative version of the TV series. The first episode, titled "Eiji 1996", recaps the first part of the series (episodes 01-24). The second episode ("Le Caine 1999") takes place after a time skip, and contains episodes 26 through 37 (episode 25 of the TV series, being a recap itself, is skipped here). The final episode, "Seal 2000", is an expanded version of the final episode of the TV series (38) and features new animation and a longer epilogue.

Frankfurt Youth team (Kubo's team while he was in Germany) comes to Japan to play a series of friendly matches. Frankfurt Captain Rudy wanted to see why Kubo left Germany to form a team in Japan so he challenges Kakegawa High to a match.

For Hikari Tsutsui, life within the two-dimensional realm is much simpler. Socially inept and awkward, he immerses himself in video games and anime, only to be relentlessly ridiculed and ostracized by his classmates. Sharing his misery is Yuuto Itou, his only friend, who wears cat ears and is equally obsessed with the world of games. After being forced to clean the pool as punishment for arriving late, Tsutsui meets Iroha Igarashi, but he attempts to steer clear of her, as her notoriety precedes her. Brazenly blunt, loathed by female classmates, and infamous for messing around with boys, Tsutsui believes that getting involved with her would cause nothing but problems. 3D Kanojo: Real Girl is a story revolving around these two outcasts—a boy full of emotions he has never experienced before, struggling to lay them bare, and a girl who strives to break him out of his shell. [Written by MAL Rewrite]

Charlotte is a girl who lives on a farm in Canada. On her 12th birthday, her father tells her that her mother, whom Charlotte has always believed to be dead, is actually alive and living in Paris, but soon she will arrive to live with them! Charlotte is very upset about this at first, but just when she adjusts to the idea, her father soon dies! Now Charlotte must face many challenges to live. She discovers that her father was from a noble family and her grandfather wants to force Charlotte to return to the family. She doesn't know her mother at all. Meanwhile, a landowner is trying to steal away her father's farm! Poor Charlotte...