Jack left Kate in the hatch to watch over Sawyer while he went to Shannon's funeral. He told her to make sure not to forget about the button. While Kate is there Sawyer wakes up, says "Why did you kill me?" or something like that to Kate and grabs her. I assume she pulled away from him and he fell in the floor and she ran out of the hatch. At some point after that Lock and Jack came back and the warning alarms are sounding.