Kokodake No Himitsu summary:

Mari Kurusu has had a crush on Kuro Rouzen (the weird guy in her class) for quite a while and when he eats her love letter she thinks it means rejection. Later she finds out his secret, that he is part of a top-secret organization that protects the humans of Earth and he brings her back to the organization to erase her memories. But for some reason, the organization choose's not to erase her memory...(from MangaUpdates)