More ideas from Tricky's bored brain

So, with news about Star Trek Discovery and bad movies on HBO, and being bored as hell at work, new ideas formed in my brainpan.

The setting is the TOS era. Something has brought a FED starship into a previously unknown star system. Depending on the way I toss around the idea, it's either a distress call or a severe gravametric disruption. Arriving in the system, the discover a massive ship (space station? construct?) that seems to be disassembling on of the planets of the system. (yes, one of those bad movies was ID4: Resurgence). An attempt to hail and scan the construct leads to an attack on the Starfleet vessel by small craft, with a few heavier ships closing in as well. The small ships (fighters, but depending on the TOS setting they might call them "assault shuttles") are difficult to hit, and harder to damage (fast with very robust shielding), and their attacks whittle down the starship's shields. Attempting to run, they detect a small group of vessels moving in to intercept, apparently coming from one of the more habitable planets, but are amazed when the new ships bypass them to engage the attackers. And they are more amazed when they get the upper hand! One of these new ships keeps sending a coded signal to the FED ship, which at first just seems to be a mathematical formula, but the Chief engineer recognizes as a shield geometry formula that would improve their current defense against the attackers.
The initial attack over, the FED ship meets with their new friends. They are very humanlike (you know, weird skin color or forehead/ear strangeness) and are very likeable, reminding many of what humans were like in their early days of spacetravel. These new aliens explain that the Construct had shown up originally in their home system, a vast distance away. Their species had just begun early travel in their home system, but were in no means ready for conflict with other species, especially one that has their own world devourer! But they had managed to get a hold of some of the ships from the Construct, and managed to reverse engineer some of their technology, using it to build their own ships, which while able to hold their own against the defense fleets of the Construct, just didn't have the firepower to do any damage to it as it broke up planets in their system. They did manage to find a way to hack into the controls of the Construct, and the plan was made to activate it's main drive (hey, ever wonder where Star Fleet got Transwarp?) and send the ships into the interstellar void.
However, something went wrong, and they were able to stop near enough to this system, regain control, and begin breaking up planets again. The friendly aliens, unable to stop it, and now locked out of the Construct's systems, picked a quiet little planet to regroup, when they picked up the FED ship entering the system.
Complicating the situation: sometimes there's a more primitive civilization on one of the planets in this system (friendly aliens will feel horrified that they have dumped their enemy on a people that can't defend itself like they tried to); a Federation or allied colony on one of the planets (they called for help); a Federation science expedition (they called for help, perhaps someone is connected to a crew member?).

So, this is where it gets sticky: Can the Starship get involved? Assuming the Construct is manned, does the FED have the right to try and stop it? Right now it's on the frontier, but if it keeps going, someday it'll be on the doorstep of a member world. But there's at least two possible Prime-Directive violations (the guys on the Construct are a society, and the Prime-Directive would say that if there is a primitive society on one of those planets they shouldn't interfere if they are gonna to die). Then, if they do get involved, HOW? In my head, they do a multi-pronged attack: using the knowledge of the Construct's weapons to upgrade the Starship's systems; using the starship's computing power and the earlier hacking attempts to overwhelm the Construct's control systems; and, eventually, diplomacy (once you've shown them that their weapons can't hurt you, you can hurt them, and now "all your base belong to us".) But then what? these guys are intergalactic strip miners; maybe you can show them how to better use their resources, but now you really are interfering in their culture.

So, thoughts?