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Republic Veteran
Join Date: Jun 2012
Posts: 78
So I've spent HOURS trying to work out what it is - its so simple you're all going to laugh.

So when you're in the Enterprise C, after you and the Timeship have made short work of the Tholians, they generally drop loot; now if you're like me, you'll be so busy picking up loot that you don't answer the hail from the Timeship, and instead go straight to the anomaly like the mission text says - however if you don't talk with the Timeship captain before doing this, for some reason the mission doesn't update properly.

So to fix it, make 100% sure you've talked with the Timeship captain before heading back into the anomaly.