The Megamishhu is produced by the NMX think tank and all round tech house MORGAN (More on them in some other submission I'm sure) and their thing is finding a better way to do things.
Namely, why bother breeding a bunch of NMX soldiers and having all those internal compartments devoted to keeping them alive in space? A destroyer doesn't need that and could be built much more efficiently as a combat drone. Of course sense you are already in the business of making custom bodies, it makes sense to use your expertise in that rather than trying to learn how to make full on robots. There are also other improvements over the basic destroyer (FTL guns, deeper description, ect) which should help GMs when they try and use NMX ships.
As far as how to use the Megamishhu there are a few things I've been thinking about for plots. Have the Megamishhu telepathically talk to -all- of your PCs with its mass telepathy organ. I know there are messages they can send that can really get under someone's skin (or even sow unrest by offering a bribe, they might start wondering if anyone has taken it up on the offer). Another idea was for a ship to get damaged, then attacked by the Meggamishhu, its starship manipulator appendages cutting into shuttle bays and airlocks so they can slide inside the ship and begin killing/capturing crew. It'll certainly be different from your standard 'intruder alert'.
Really, this isn't intended to be an NMX plotship, just a destroyer replacement designed to flesh out their attack forces a little bit. Boarding ships, plot elements, and whatnot should take place on the NMX ships designed to carry people. If you want a plot point you should probably hold off until I make a writeup for MORGAN.