Pretty interesting, I really like the cold opening. Here's some simple editing suggestion:

"They were living in the brightest, most vibrant centre in the universe, yet they were kept in the dark." (Paragraph)

"The Stellar Capital was the largest gathering of interstellar civilizations, a diverse metropolis of intelligent beings from all across the universe. Its citizens were amongst the highest ranking intellectuals in history, and even they didn’t know. It has the kind of security that the entire Andromeda galaxy couldn’t afford, yet the "?" had gotten in."

You should give it some kind of identifying noun, some hint of what IT is, because you need to lure the reader in more at this point. Even something like the invisible threat, or unseen adversary, etc.

"Only then will they understand, and once they do, they will be crushed by their impending fate. The citizens will be blindsided and turn on each other. It will over as soon as it begins. For once, the balance has shifted. A new dawn is rising."

Very good except for that last line, it's just extremely cliche. Also, what balance? Have these invisible things been living in balance with intelligent life, or did the phrase just sound good? You should ask yourself this, in case there is a stronger ending. I would like to have some idea of what the antagonist is, but none of these lines hint towards its goal or purpose. Still, the opening is very good and establishes a strong tone and premise.

Part 1 flows well, just need to break it up into paragraphs. I like how you subtly joke about aerodynamic space ships, small details like that give the protagonist more character than anything IMO. Keep writing, this seems like an interesting tale.