The Black Lotus — Kieran Fanning

Ghost, Cormac, and Kate are not like other kids. Ghost can turn invisible, Cormac can run up walls, and Kate can talk to animals--all abilities that make them perfect for the Black Lotus, a training school for ninjas who are sworn to protect the world from the evil samurai-run Empire. But when the Moon Sword--a source of unimaginable power--is stolen, the three are forced to put their new skills to the test and go back in time to sixteenth-century Japan and retrieve it.