This is a great concept for a mission. However, it felt a bit too long.
Some stuff to consider cutting: The prisoner transfer really didn't drive the story. It would be understandable if it was Amar Singh and you get to see him. Otherwise it really served no purpose to the story.
The shuttle was not needed to drive the story. Having to pick it up really made no difference in how the story unfolded. The using it to get to the planet didn’t really work well because you actually beam in. If you really want them in the story we shouldn't need to pick them up.
Entry into the Beytan System: You should advise of the arrival at the system. Then let us enter the system where the story starts. The button should say "Enter the system" or "Drop from warp" along those lines. Not “Retrieve the shuttles”. Once in the system have the player travel a short distance to rendezvous with the USS Nautilus as described in the earlier instructions.
Interior of Ship: Well designed considering what you are given by the Foundry to work with. As mentioned above this set would not be needed if you cut the prisoner transfer.
Beytan Space: The person that shows up on the screen as the Nautilus Captain appears to be one of my tactical officers. Upon reaching rendezvous with USS Nautilus there is a cargo frigate and the dialog states he is warping in. Previous dialog said they were heading to the rendezvous implying he was already in the system
Damaged warp core on the USS Zues? I’m sure you meant “USS Zeus”.
After transport of prisoner one of my tactical officers shows up again as the captain of the USS Nautilus.
Upon activating Phaser 2 there is a warp effect before you actually warp. It made it a little confusing visually.
Unknown System: In the report by my tactical officer the second line states that "Internal ship scans are not picking up any unknown life forms." It just seemed a bit odd.
The Dialog buttons during the effort to destroy the nanites should be something other than "Continue". Consider using some of the following; "Recommendations", "Report" or even "Maintain frequency modulation". You get the idea.
On the Station: This was really well done and should be gotten too much quicker. I like the “infected crew”. Well done on them.
Unknown System: Liked the fight. It kept me interested.
See if you can align the course forced by the game for warp with the warp conduit. It would look much better. The one from the Beytan system looked great.
Unknown Planet Space: Shorten distance to travel but otherwise this was really well done too and should be gotten too much quicker.
Ancient Times: Excellent design. Good balance of fighting and mission tasks. This was really well done too and should be gotten too much quicker.
Singe, Sing or Singh: Really great design and execution. This should also be gotten too much quicker.
Summary: Great concept! Excellent writing and set design. I loved the "infected crew" design and execution. However the mission felt a bit too long. Also, too many "Continue" buttons. Consider other button responses for those. Overall, great job! I look forward to playing part 2.