The multiple arcs are part of a single discontinuous time-line.The large wind turbines that are ubiquitous through-out the anime are actually aliens with powers over time and human emotions. They are conducting an experiment with the protagonist, Junichi Tachibana, by manipulating events to pair him up with various girls. Events are allowed to proceed to a conclusion, then the aliens rewind time and begin again with a different girl. If only Junichi had a friend with a big blue box...
All this happens in a computer mainframe, the characters are AIs and their world is simulated.Think about it. The first two simulation runs (Haruka's and Kaoru's arcs) seemed normal enough, because the AIs and hardware are still fresh, and they behave like how they are meant to. By the time the third run (Sae's arc) came around, errors had accumulated in the main memory and cause the AIs to behave more erratically. Junichi's AI may have even gained self-awareness, due to the recent awakening of his Genre Savvy traits. The Lemony Narrator is probably created by the system to ensure that the breakdown can be contained.