A beautiful game; well done.
A couple of notes, though; some on bugs and some on game play.
First, the game play. I loved the beginning where the missions were actually challenging but completely doable (as long as you spend more time dodging than killing), the difficulty was perfect, but after just a few upgrades, namely the reg. ones, my ship was virtually indestructible. By the time I'd completed ~12 missions I didn't even really bother dodging anymore because I was healing faster than I was taking damage. After that the missions were monotonous because they were all too easy and I collected upgrades only out of compulsion because I was already as powerful as I needed to be. More balanced upgrades, or far more powerful enemies in later levels, would have made the game a lot better for me.
Second, this game still has the occasional bug; here's the ones I found if you're interested in doing another update.
When I loaded the game after beating it I was taken to the game-over 'scene', which isn't ideal in my opinion. Then, when I started a new game after beating it once, supposedly overwriting the old save file, I got to replay the opening but my ship was already maxed and when the opening finished all the missions were already beaten (also, Occator Prime claimed to have -3 upgrades available) so for some reason it didn't really start a new game.
Two other small bugs: the game froze on me several times just as I completed the second scanning mission in the Razna Convolution; I tested this on Chrome & Aurora and got the same result. If I clicked outside of the game, pausing it, when I unpaused it it would advance a little bit and after doing this several times it got over it.
Also, after completing all mission and gaining all upgrades (except the final mission) there were still 2 missions listed for the Nyx Conglomeration that weren't really there (I searched quite thoroughly).
Criticisms aside, it really is a fun shooter, though, and the story aspect is well done. I congratulate you again on making it.