After she arrived in the real Karakura Town in Soul Society, she confronted Aizen & Ichimaru. She stopped Don Kanonji from attacking Aizen, thus saving the Human's life. Ichimaru then took her to a rooftop and talked to her briefly. He then said she was in the way and stabbed her in the upper chest. He tells Aizen that he killed her and Aizen notes that her reiatsu has vanished.
It is later revealed that Gin did not kill Matsumoto. He instead knocked her out with the Kido Hakufuku. She rushed to his side when she awakened and was found by Aizen, who is interrupted by Ichigo's arrival before he can do anything to her.