Polite and kindhearted Yuuki Ashikaga meets Kotonoha Katsura in the school library and develops feelings for her; unfortunately for him, Kotonoha has just started dating Makoto. When Yuuki happens to find out that Makoto is seeing Sekai Saionji in secret, he feels compelled to put a stop to it in order to help Kotonoha. Unfortunately for Yuuki, a lot of complicating factors come into play, from Ai Yamagata deciding to try and win Makoto for herself to Roka Kitsuregawa developing feelings for Yuuki, and thus begins yet another tale of high school romance, poor communication, and morally reprehensible people.
Cross Days has also been adapted into a two-volume manga, with a more simplified and streamlined story and Makoto somehow being even more of a total jerk than ever before.
- Adaptational Villainy: Amazingly, the manga adaptation manages to top the School Days anime in terms of portraying Makoto negatively. The notoriously insensitive Makoto goes from being a libido-driven idiot to an outright sadistic Manipulative Bastard and Attempted Rapist who is almost as bad as his old man.
- Adapted Out: Several characters and a lot of plot threads from the game are not present in the manga.
- Ascended Extra: Ai Yamagata is elevated from minor character in Summer Days into (unfortunately) one of the catalysts of the Love Dodecahedron of Cross Days.
- Blackmail Backfire: Yuuki's initial plan to stop Makoto from cheating on Kotonoha is to take inappropriate pictures of Sekai, the girl he's cheating with, and use those to blackmail her. This backfires spectacularly when Setsuna catches him at it and forces him to crossdress as punishment, which is how the whole Yuu disguise gets started.
- Distaff Counterpart: The game introduces Hanon Nijou, the elder sister of Kazuha and Futaba from Summer Days, who is a counterpart of Makoto in term of Really Get Around due to her numerous sexual partners.
- Eviler Than Thou: Oh boy, Kasannoin makes even Makoto's infidelity looks tame by comparison.
- Gay Option: Yuuki and Makoto can end up together.
- I Want My Beloved to Be Happy: Yuuki's goal for most of the visual novel is to help Kotonoha by stopping Makoto from cheating on her, even though he has his own feelings for her. This can be subverted if Yuuki decides to pursue Makoto.
- Idiot Ball: Not knowing that Yuu is Yuuki in disguise is one thing, but not knowing that she isn't female while having sex with her is another level of idiocy.
- Love Dodecahedron: Yuuki likes Kotonoha first but then falls in a mutual love with Roka, Kotonoha and Sekai and Ai all likes Makoto, Makoto can fall in love with "Yuu", Nanami can be "comforted" by Makoto if her boyfriend's infidelity is revealed. Niki, Shibukawa, Ion, and Yoka and Ai all can be involved with Yuuki, Hikari likes Taisuke, Taisuke likes Kotonoha but can reciprocate with Hikari or go become even worse and rape Yuuki as "Yuu", Tanaka likes Setsuna, and Uzuki and Yae are involved with Kassanoin. In fact, it's pretty surprising that the local Femme Fatale Hanon is not involved in most of these problems at all.
- Multiple Endings: A whole bunch of them. Unlike the first game, though, it doesn't have any of the same violent bad endings that made the original game so infamous. There are, however, still a few that involve Kotonoha snapping and murdering someone.
- Only Sane Man: Yuuki is one of the few people who bases his actions on any sort of logic, which is enough to make him stand out in a series like this. It ends up getting subverted if he pursues Makoto.
- Took a Level in Jerkass: Taisuke was never a particularly nice character in the original game, but he's noticeably worse in this game, in which he and some of his friends blackmail "Yuu" into sex.
- Your Cheating Heart: Yuuki gets involved in the plot when he finds out that Makoto is cheating on Kotonoha.