Zannen Kunoichi-den

Reika isn’t just a high school student; she's also the military’s secret ninja agent. Transferring to Seiou Academy is part of her mission to locate a person of interest. It just so happens to be her sister Michiru, who has gone missing, and finding her is critical to saving the nation. Reika thinks her mission is complete when she meets Aoi who looks identical to Michiru but finds out otherwise. But when she learns about a kidnapping threat meant for Aoi, Reika can’t help but get involved in protecting her classmate.

(Source: MangaHelpers)