It is implied she was victim of domestic abuse at the time of contracting. In conjunction with Ito's health it is not surprising she was in the psychological state to contract. Since the MSY was still very much a clandestine organization she was forced to discard her public persona and go missing, sadly enough with only a written goodbye to Ito.
Little is known what she did in the coming years, but by 2065 she was discovered by Ito, now inspector at the police, during an investigation in the missing girl case of Okamura Yuu—actually a new contractee. Forced to an informed decision Aiko's superior, Sakura Kyouko, gave her the chance to introduce her former love into the MSY.
Her current status is generally unknown, though she is alive and makes an appearance in Chapter 34.