I actually don't like this story. Not that it isn't well written, as it is, and not that it is not thought provoking, because, again, it is, but because I truly hate to see Harry go dark. (I also usually won't read slash, or Harry paired with shudder Pansy.)
Your story begins with a standard 'Harry gets set up and everybody including HIS TWO BEST FRIENDS desert him in a heartbeat. (I never can understand that!) Sometimes I wonder if the wizarding world is too stupid to survive at all. No, make that all the time!
As Signior Benedick said: "It is too short for a tall praise, too plain for a grand praise, too brown for a fair praise and were it that which it is not, and not that which it is, I can say that I like it not." Or something of the sort. Shakespeare was never my strong suite.
Grammatically, There are a couple places where the wording is kind of dicey, you'll use the same word twice in the same sentence with each repetition having a slightly different meaning, such as: "A blood soaked shadow that sought to consume the world in it's all consuming rage." Mebby a better choice would have been: "...engulf the world..." though I like the 'blood soaked shadow. Mind if I steal it? There are only two other examples of that type of bumf here, so I can say your writing is better than mine.
My other complaint is that you never really explained how Harry/Darth Dion managed to build all this neat technology, other than the crystal in his Lightsaber.(Nice touch, that.) Current technology will not support the repulsorlift systems that the LAAT's, Torrent Fighters and Nova Wings require. Not to mention the infiltrator is a unique craft relying on technology that does not yet exist. Also, where is he going to put a thirty five hundred foot long star destroyer?
This has a strong potential, with some polishing, to become a great story, and for that I shall set aside my dislike of a(n understandably) dark Harry and continue to read.
I have placed this on my 'alerts' list and hope to read more soon. Alorkin