Did a playthrough of the map today, and while it's not perfect (no map is!) I enjoyed it.
Story
Honestly, I don't think a map needs a good story to be a good map, and chances are trying too hard to make a good story will just end up making it worse. This story is good enough for a map, but having the virus, the factory and the governor's story a little more fleshed out, which basically means including more story elements around the map, would not hurt. My biggest gripe here is that some signs have pretty poor grammar, which makes them annoying to read. Fixing these signs would make the map a thousand times better, story-wise, along with making the map feel a lot more polished. (NOTE: using TEdit for this will save a lot of time!)
Gameplay
The boss fights, except possibly Queen Bee and Destroyer, were very easy. This doesn't have to be a bad thing, as it makes the map more accessible to new players, but it can make it boring for more experienced players, which the majority of map-players are. Also, be careful if you decide to buff them - a very easy boss fight is more fun than an impossibly frustrating boss fight that will force most players to cheat. Perhaps you could release an alternate version of the map with expert mode?
As for the rest of the map, it's not that special. It's a little too short and a little too easy. Most puzzles can be solved by just shooting a button once or twice which can make the map boring for many. Personally I'm not a huge fan of very difficult puzzles, I prefer more adventure-ish maps, so this wasn't an issue to me. However, it might be for others. To summarize, the map is too easy and there are too few challenges around. Some more parkour, for example, would be nice!
Optional side quests! I love them, and I'm glad there are some. Some non-boss side quests would be cool, like parkour quests for example. I like how the side quests had a story as well. Keep this in mind when/if you make your next map.
Usually maps have a few hidden secrets, like hidden chests with diamonds, wacky fun loot or something. Of course this isn't a must, but some hidden chests are always nice.
Building
The builds in this map is good, especially for your first map. The use of details is great, I love the style and the use of monoliths for the background. Also, creative use of the conveyor belts in the ending!
Bugs/Issues
There is no mechanical worm in the Destroyer boss fight room, at least I did not see one. I cheated one in.
To the right of where you enter the jungle area there is an unescapable hole.
Summary
The map is pretty good, especially for your first. The most glaring issue is that some signs have poor grammar, other than that the map is fun and well made. The boss fights are a little too easy, as is the rest of the map, but it does not make the map unenjoyable, at least not for me. Higher difficulty would make the map more fun.
Building is great, keep that up.
Welcome to the mapping community, I hope to see you around!