The only thing worse than not finishing your sampling run was being captured by Imperial soldiers. Fortunately, your team has escaped from what passes for a cell.
Now you just have to get out of the Imperial fortress, find your way back to the Xenogate, and return to base. It would be good to stop at the anomaly site and collect all the data recordings, too.
Hm, I wonder why that Imperial Legate was so interested in the anomaly site? Maybe you should figure that out too. It's bound to be something bad...