Enigmatic Fortress ironman glitch

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Accrsd

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So i have an ironman save right now where i've defeated the fortress and got all the way to the end.. while this was happening i decided to take my science ship and explore the system.. which was apparently a mistake because now when i try to finish the chain with any of the science options it keeps telling me i have no science ship in orbit.. i can just send in a fleet and do that part just fine but i can't get either of the two science ends to come together, any ideas?
 

Accrsd

Colonel
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Mar 9, 2012
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whenever my science ship is "in orbit" of the fortress it doesn't register as such in the situation log. And there's no way to "research project" on the map itself so i assume it has got to go through the situation log.. i'm just afraid i've botched the whole thing because i said.. ooh look.. candy and went to explore the system mid event chain. though that said a few new tombworlds wouldn't be particularly terrible but i was hoping to get the more meaty rewards