This explanation also fits well within the confirmed story because now, instead of the gun miraculously being recognised as something 'important' by the Citadel security system, and thus not being destroyed (which would nullify our chances of advancing further), it would be sensible to suggest that the security system recognised a piece of Combine equipment and simply 'charged' it up to its full potential, now capable of manipulating pure dark energy - something it was originally intended for. The audio files from the leak explain - without contradicting what we have in retail, instead supplementing it - that Eli built it using Combine tech that Alyx brought in from one of her scouting trips. Marc Laidlaw recently did confirm that Eli made the gravity gun post-incident. Except your fanfiction doesn't rely on any existing info from Valve-produced content, and contradicts what's already in the game (Alyx saying they use the gun to clear minefields, clearly suggesting it's been in use for some time already).

Half life 2 cremator