Welcome to Dakka.
Dealing with the huge scale of
40k while keeping it focused is something that can be pretty difficult, especially when dealing with
IG, the most numerous faction (besides nids, and I can't see a Gant telling a story

)
The key thing is to decide what you want from the piece: Do you want an all-out action thriller, or something more focused on character? It seems like you want to go for the latter, and my advice would be to keep it simple. All you need is a couple of lines about the scale of the operation, maybe some vox-chatter from other units in other pars of the ship, and then focus purely on the characters. The reader, if familiar with
40k fluff, will know that anything involving the
IG is on a huge scale, so you can kind of assume that you don't need to bring it up that often.
Think of it like 'Saving Private Ryan', if you've ever seen that. Everyone knows that it's taking place amidst a huge-scale military operation, but you are more invested in the character's personal stories so the film focuses on them, only dropping hints now and then to what's going on around them. In the same way, create some characters in your squad that people will be interested enough in that the larger operation doesn't matter so much. Make the opp as a whole a setting, rather than a story.
Resist the urge to plunge the squad straight into combat. Build up atmosphere, character and setting so that when fighting does happen, it means something other than 'let's kill aliens'.
The other thing I'll mention is that the community here is usually very helpful and willing to offer advice or criticism on work once it's up, so the best you can do is draft the story and post it, and people will be able to give you feedback that you can then act on. It takes a while to really get the feel for
40k, so your best bet is just to go for it, post it, and redraft it once you've had feedback.
Best of luck.