Ok four things.
1. Did you wait until you picked up the scientis?
2. Did you destroy all enemy ships?
3. Did you go to the center of the nebula's?
4. Did you respond to all messages sent to you?
If you did all of those things I can't think of a reason for it to malfunction like that.
To Mankind
And the hope that the war against folly may someday be won, after all
Isaac Asimov