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The war has just ended in a great victory, the Empire is celebrating, the people are rejoicing.

But the entire fleet, and a science ship are "Missing in action".

Our commanders are worried, the Empire is defenseless, what will be the fate of our fleet?

EDIT AFTER ANSWER:

There is a MIA icon on the top notifications area, hovering over it tells what the arrival due date is. Adding MIA due date information:

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  • Think I had a science ship go missing in action once. There was a mission in the situation log to check some systems and find them. One was friendly space, but not so friendly I could get civilian access, and I never found out what happened to them. – DCShannon May 24 '16 at 18:00
  • @DCShannon: Sadly there isn't any note in the logs. – ShloEmi May 24 '16 at 18:07
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    UPDATE: The fleet safely returned to the nearest planet they could find. It took them few months. [rubbish alert] Shared their return adventure in the local inn. The empire decided to give them all a 'War hero' medal and a few days to rest with their families in any planet they choose. – ShloEmi May 24 '16 at 19:04
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It means your ships had nowhere they could legally be after the war ended, so they are making their way home individually.

When a war (or access treaty) ends with your ships in a now illegal position, one of two things will happen. If they can move to a legal system, they will travel to it on their own. You won't be able to control them until they get there, but it's usually very quick so hardly ever an issue.

However, if there are no legal systems to move to (happens most often with hyperlanes, if the system and all connected systems are now blocked territory), they go "Missing in Action". They will slowly make their way back to your Capital and reappear after some amount of time. The tooltip over the fleet will tell you when they are due to arrive.

A science ship going missing during an investigation is an event, and not related to military ships going MIA after territory access rules change.

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    Sorry to be pedantic, but isn't this the exact opposite of missing in action? Since the situation arises after a treaty, the ship only goes missing after the action has concluded. – Superbest May 24 '16 at 23:18
  • It is also possible to go missing in action without war or access rights change involved - you can be two systems deep into someones territory before you encounter any of their ships, and the borders appear only after the first contact. – Deltharis May 25 '16 at 8:04
  • @Superbest "Missing in action" is generally used when a person or ship is outside of friendly space, either going to, being in or returning from a mission area - in contrast to being stolen from dock for example. As far as spaceships go I'd say anything except orbiting a planet or being repaired is active. – Annan May 28 '16 at 7:55
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When you lose travel access to a system your fleets are occupying, the fleets will become "missing in action" for a period of time before they go back to a point they can access (I don't know exactly how this is determined, it seems to be the closest system with a settlement). You can see when they will arrive if you hover over their icon on the fleet menu on the right side of the screen, or the notification box at the top.

It seems like the time it takes for them to reach their destination is longer than it would usually take if they were being controlled directly, but I have not verified that.

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