I figured after a week with your mission up you deserved at least one play through so I had at it. I know what I do is I have my friends and fleetmates play through my missions when I make them, it helps get them out of review limbo as well as gives me good feedback! You should try that! If you don't have a fleet, pretty soon every fleet will be grabbing up whoever they can. Definitely will find one then!
First off, these are all suggestions. Do with them what you will. You have some good meat and bones in here, which is much more than many first time authors. For dialog errors and focus on making it flow, you already have a review pending from Evil70th! He does a good job, so I will leave most of that stuff to him and his review!
Rename the First Map "Go to K-7 in (whatever sector block) and continue to Jaroana" This is important, as it will list in the objectives where players need to go. This is the first and biggest mistake first authors make. Players are morons, they will forget where you told them to go. Make it obvious.
You may want to tone down on some of the ground enemy combat levels. I fought a few commander level and/or captain level mobs, I suggest lowering that down a hair. In addition, the final security team hallway could do the same purpose with half of what they have. Just spread out the mobs a bit to make it look like more.
You may want to expand the reach marker on "find Shryoana(or however it is spelled)" in the base, or put a larger nav point marker on her cell. As it is currently, I ran by her and had to go back, the current small size made the location difficult to see on the map. That or make an object interact for each cage, so the players get clues via scan area.
Additionally, put a door in the way at the end of the cage room before the security hall that you can have opened after finding her. I suggest using "Science Wall" and having it set to go invisible after. It looks like a door if you center it right.
Was there a romulan in the base? Or was I supposed to go back and talk to the "spikefaceman"? I never did. Also how did "spikeman" live that long? Did he explain it? If you want us to talk to him, give the cage controls in that room with them. Expecting us to go back after we "trigger the events at the end of the map" is not going to happen for most people. There is suddenly a very big problem that needs to be dealt with.
Those are the big things, now for smaller things I have that may help.
Think of a good brief for the mission description that people search for. As is, what little is there is great, (and beautifully puny after playing the mission) but does little to grab players attentions. Think of a way to expand it a little bit to add more attractive flair than farmers missing. You have much better things going on in this mission then that McGuffin!
You never actually named the race who made the base, which is good, but... you made some implications that it was perhaps the group tracked down by the Ent-D. That would make them the Iconians and would put you in dangerous territory. Mainly because they are being set up as STO's main badguys by cryptic. At least, thats who I thought you were trying to reference. There is, technically, nothing wrong with that but... it puts you in dangerous water involving how their empire fell and what they actually were if and when Cryptic gets that far with them.
I suggest (only suggest) you go easier on that Ent-D reference and just make the race another of the large scale but long forgotten Galactic Empires of yore. It will allow you more play with them and creative freedom (I liked the hints and reasoning for their genetic manipulation you suggested!). Romulans are always after old tech, so, they would still be interested! Just a thought that wouldn't be hard to make, you just need to remove your one Ent-D reference. (It's okay though because your Enterprise (NX) reference is good and supplies plenty of touch-stoning).
There is your feedback! With some work, plus what Evil70th will give you will definitely improve what great work you've put together. (Oh! Warning, he doesn't like the Continue button in dialogs, but, if you read some of his reviews you can catch his ideas on that. Your's does that a lot, but it is in no way a game changer. Just giving you heads up)
I loved the maps, especially the revisit to the surface, and the explosion at the end was fantastic and honestly made me jealous. You'll get five stars just for that!
With work, your mission will be solid 4 star or better IMO. Much better then the simple name or mission brief description suggests! Keep the title, spice up the description. You'll get more players finding out how world shattering it actually is!
The old empire is the Chodak, from A Final Unity. As I couldn't get a clear answer on if it was ok to use people and species that only appeared in other video games, I did what Drogyn1701 suggested, and just put in suggestions to the game and species, like Optimator and Allanor being half corrupted in the logs, and the Romulan interest/Enterprise D's mission, referencing that game. The final nod was the name of the new species. It's close so if people have played that game, they can make the connection. If not, then at least they will have some backstory, without possible IP infringments.
The Romulan was in the cell beside Shryana. He's on the ground, holding his head, and is the same model as all the mobs. You were not meant to go back to Spikey guy, as things moved on, but I wanted to introduce him somehow, just so it wasn't a completely who the heck is this guy moment at the end. I'll rethink about his dialogue, and that end bit, explaining he was newly created. As for Shryanna's marker, I didn't put one on. I was thinking the players could investigate the cells to find her, although she is the only one actually motioning for help, as a bit of a clue. I'll make the marker visible, and may actaully redo the entire holding cells entirely now I've got my feet wet. Make spikeyguy and the Romulan a bit more noticable as well.
Yeah, I was thinking I may have overdone it with the end mob, but was waiting for some feedback before I changed that. Odd though, I had thought I'd put in no higher than Lt for most mobs. I'll be sure to tone that down.
I've written quite a few fan fics in the past, so I'm in the habit of not wanting to spoil things for the players. That's something I guess I should work on for the write ups and whatnot. Making missions is quite a bit different than writing stories. Thank you for playing, and giving me all this feedback. It's highly appreciated.