I really enjoyed reading the first couple of chapters. Your characters are three dimensional and engaging, and you put together an interesting crew. But I have to say you switched me off right when you described the Starfleet Cube which is so big it's a little ridiculous. I understand where you're going with it, but I won't be reading more, sorry.
The Starfleet Cube design is interesting because it surprises me. Fleet ship designers have evinced an enduring fidelity to the aesthetics and ethics of their the Federation. Starfleet ships are not painted with dark colours, always that almost white, silvery duranium. Fleet ships almost always have the bridge situated on the top of the ship, flouting obvious danger. Fleet ships--even attack dogs like the Defiant and Akira classes--do not have massive, martially ostentatious weapons arrays. Fleet ships boldly broadcast the Federation/Starfleet ethos of peaceful exploration; sword/phaser sheathed/holstered, but with, as the Capellans say, open hands and open hearts.
I cant wait to see what happens when one of the DQ powers (let's say the Voth) mistakes the Tesseract for a Borg Cube.