Several scenes, events, arcs etc occur in a non-chronological order. This means that for the majority of the story, the order at which events are told does not match the order at which they happen.

Two examples of this (from anime) include The Monogatari Series and The Melancholy of Haruhi Suzumiya. Where many events are told indifferent to their chronology.

Note 1: Do NOT include one-time prequel events or backstory arcs. A good rule of thumb to know if something could be considered "non chronological" is if in most cases, you need to look up a timeline guide.

Note 2: Do NOT include VNs that JUST have branching plots, those are still chronologically-told stories according to ONE out of many timelines.