After I clear the U.S.S. Kirk bridge I can't speak to Captain Thelin after I find the Temporal agent. I tried it a second time and I still couldn't speak to the captain before contacting the agent.
Same happened to me, but I was still in the mission while I looked here for answers and while I was away the mission progressed and allowed me to talk to him. Just had to wait for a while. Give it a try and see if it works for you as well.
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original join date 2010
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Edit: Yup, give it a minute or three. He'll come around.
Apparently the level designer expected us all to talk to the captain first, before unlocking the probe