Great Story Badger, I hope you get over your writer's block soon. I too like many others came to this story after finding Polly mentioned on tvtropes. I just spent the last week or so reading all three stories and enjoying them immensely. I have a few minor nitpicks though. Just an FYI you should never feed a dog chocolate, it contains theobromine which is fine for humans but poisonous to dogs, something Polly would surely know.
The only other nitpick I have is with he Broken Bow story. I would think that every torpedo made by UEMA would have a serial number traceable back to the ship it was assigned to, as well as individual component with their own serial numbers. if a Torpedo were found to be lacking those serial numbers, or had serial numbers that didn't match, or matched a known torpedo still in inventory on another ship, or in a warehouse somewhere, then it would be known to not be of UEMA origin. Even were someone to tear a torpedo apart and remove every visible serial number (a lot of work for something that is going to be vaporized anyway), the actual chips themselves have identifiers under the casing, as well as being traceable to a particular model and revision number, as well as the batch based on the components. That is why the ATF loves unexploded bombs, even when they go off they leave lots of evidence behind. They should have been able to say "this torpedo was lost with the (blank)" or "this torpedo shows to be on the (blank)". Weapons like that leave a trail, and the lack of a trail itself is a huge clue to it's origins.
Like I said, a minor nitpick because the story moved along fine without it, and I hope you don't interpret that as negative feedback. I love the story and the characters and I feel that you have done a wonderful job making them seem real. Please do continue. I await anxiously your next installment.