Before I get started, I'd like to address some reader concerns:
Yes. SotS is quite underpowered for what they are canonically capable of. I wanted this to at least be something of a 'fair' crossover, and that's actually very hard to do with SotS. Their tiny ship size and huge firepower (Cutting Beams = Shadow Beams from B5, holy crap) mean that they can kick a lot of ass in universes like Star Wars, Halo, and Mass Effect, where you have kilometer long starships that don't mount half that. It's largely due to the difference in genres. 4X games usually have strong tech advantages over their FPS and movie counterparts.
I would say that Mass Effect is being sold short a little bit, but rather than start an argument (there are forums for that), I'll just say that in order to keep the threats, you know, threatening, SotS has been nerfed, and Mass Effect has been bumped up a bit.
That said, here is a story (gasp, an actual story, my god!), wherein the Liir will demonstrate exactly why you do not tick off a race with fusion weapons. I do try and proof my stuff, but some typos are bound to slip through, as I am lazy and would rather be playing than proofing. If you find a typo, post it in a review for me to fix, and go get yourself a cookie of your choice.
"Well, this is dull," grumbled Captain Vorhess as he watched the planet Lorek spin lazily below from his command chair. "Ensign, tell me you have something. All this 'patrolling' is making me want to quit the Navy and become a mercenary."
"Sorry sir," the young Batarian manning the sensors replied. "Local forces have contained the plague riots, and since the planet is quarantined, there's been no ship traffic for days."
"Wonderful. I finally get promoted to captain, and they give me a frigate command in the ass end of nowhere. I have to run all around the system, looking for 'threats'. Meanwhile, the mighty commodore gets to sit his cruiser in dry dock because of 'plague contamination' and have some Asari slave girl serve him honey mead in his luxury suite. Makes me sick."
"Captain, are you sure it's wise to- Sir, new contacts! Six unidentified frigates! They just appeared next to Hammer Station!"
"Frigates? What the hell are-"
"Positive IFF! They're registered as Liir cruisers!"
"Oh no.." Vorhess said in a low tone, zooming the ship's holographic display in on the ships with a wave of his omnitool. "Get us out of here! Maximum speed out of the system!"
No sooner had the captain spoken than there was a brilliant flash of light from outside the ship. A shower of glowing yellow bolts poured from the Liir ships, passing through its barriers like they weren't even there and hammering into the armor. As the lights faded, it looked like the station looked like wax brought too close to a flame. Huge swaths had melted away, and the rest was riddled with melted holes each size of a small shuttle. As Vorhess watched, something exploded deep inside the station, and about a third of it broke off and began drifting away.
"Maximum speed, aye!" the pilot replied, and the rest of the crew seemed all too happy to let him plot a swift course away from the battle. Many of them had friends who worked side jobs as pirates in Liir space, or had even engaged in some piracy themselves. There was no way they wanted to be in the path of a Liir warfleet, not when their own cruiser was sitting helpless in the burning wreck of the station's drydock.
"Sir, twelve contacts entering the system! Liir destroyers!" the sensor officer cried, and their icons instantly appeared in Vorhess' display.
"Make for Dorgal, we can lose them when they slow for the planet's gravity well," Vorhess ordered, pulling up a display of several the ships that had started moving toward them. Something looked off... "Belay that! Full evasive! Those are torpedo ships!"
The captain felt a sickening pull as the ship's inertial commentators tried to adjust for the tight roll their pilot was attempting to pull off. He almost made it. Several of the torpedoes flashed past in arcs of crackling white light as they chased the ship's countermeasures, but the pilot couldn't adjust for the ship's momentum. The frigate slid sideways, exposing part of its flank to the enemy ships. To the Liir gunners, it was a target they couldn't possibly miss.
The ship heaved as a torpedo slammed into it, crashing into the frigate's flank. Pain blossomed as Vorhess was thrown from his command chair to the floor. Wiping blood from several of his eyes, Vorhess saw the ship was now running on emergency power, and judging by the weightless feeling in his body, the gravity appeared to be going out as well. Somewhere, a warning Klaxon was blaring, and he thought he could hear someone screaming in pain, though the way his ears were ringing, he couldn't be sure.
"Damage report!" he bellowed into the chaos.
"Engines are offline," said a voice from somewhere behind him. It wasn't his Exo, that man was laying dead over by the windows, which Vorhess noticed with some alarm were heavily cracked in several places. Fortunately the armored shutters had closed over them, keeping the atmosphere inside. "The core is intact, but the mains were mostly severed by that last torpedo. Until they can fix them, we've got no barriers or weapons."
"Damn it," Vorhess snarled, climbing shakily to his feet and waving his omnitool at the main display. It sputtered and refused to engage. Enraged, he kicked it savagely, and was satisfied when it flickered to life, showing the Liir destroyers holding their position some distance from his battered ship. "How long for repairs?"
"Not sure," said the voice, and now that his head was clearer, Vorhess recognized it as belonging to the ensign who normally crewed the sensor array. "They say they're going to try and get engines back online, but depending on the damage, it could take hours."
"Damn those overgrown fish. Why don't they just finish us off?" Something clicked into place in the captain's mind then, and his eyes widened. "Ensign, get me engineering, on the double!"
The young batarian pressed several buttons on his terminal, and when nothing happened, pulled up his omnitool and fiddled in the air above it. A series of sparks flew from the terminal, and Vorhess heard the voice of his engineer over the speaker.
"Captain, I'll have engines for you as soon as I can. Half my team is dead and the other half injured. This is the best I can do"
"No, stop your repairs. You engage those engines and we're all dead. I need you to shut down the core."
"Shut down the core? Captain, are you insane? The Liir-"
"The Liir are waiting to see if this ship is still alive, or just taking its time about dying. As soon as it becomes obvious we can actually fix this damage, they'll fire another volley and finish us for good. Our only hope is to cut all non-essential power, and hope they find something else to shoot at."
"...alright, sir. You'll all want to put on suits, I'm going to have to cut power to life support too. Engineering out."
"Captain, I have a camera feed to Lorek. I think you'll want to see this," the ensign said as soon as the channel closed.
"Put it through. Let's see how our dear friend the Commodore is doing." The main display switched to a slightly out of focus shot of the planet behind them. Hammer Station was nothing but burning wreckage now, and Vorhess thought he saw the prow of the commodore's cruiser drifting in the ruins, but it might have been his imagination. He also spotted debris fields at the last known positions of the other patrol frigates. Apparently they hadn't fared any better than his had.
As he and the rest of the bridge crew watched, a trio of destroyers began approaching the planet. Each fired a single large missile before the entire enemy fleet turned and started moving away from the planet.
"No radiation or energy signature from the missiles," the ensign supplied helpfully. "They don't seem to have any kind of payload..."
"Bio-weapons. It's a damn plague fleet. They'll wipe out every living thing on the planet with those!" the captain snarled, pounding his fist into the projector and causing it to spark and die again. With a sigh, he hung his head and spoke softly. "Everyone to your suits. Engineering should be cutting life support any time now."
No one spoke as they all climbed into their environment suits. It would have seemed wrong, somehow. What did one say after watching xenocide?
Bulky suit creaking in the silence, Vorhess sat down in his command chair (the arm had been torn off, he noted with a grim bitterness). No sooner had he done so than the lights died, and he started floating up into the air. Wearily, he belted himself down and turned to the crew.
"Someone go down to Engineering," he ordered, his voice flat and exhausted. "Tell them to do what repairs they can without power, and to fire up the core only when our suits are about to give out. I'm not taking any chances."
"What then, Captain? Set course for Khar'Shan? To warn them?" the ensign asked, and Vorhess was grateful for the helmet that covered the young batarian's face. He didn't think he wanted to see the expression.
"Khar'Shan will know soon anyway, if they don't already. The Hegemony is about to be paid back for every raiding vessel we sent into Liir space," Vorhess said darkly. "And it appears they are big believers in interest. When we have power again, if we aren't dead, set course for Omega. We'll try and figure out what to do when we get there."
Silence returned to the bridge as far behind the crippled ship, a world full of 5 million dying souls spun quietly through the stars.
Following the Batarian Extermination, several Batarian ships that had been listed by both sides as destroyed in action were unable to be located by salvage teams. It is unknown if these 'lost ships' were merely taken by rogue scavengers who left no record of their haul, or if the ships survived to lip away, seeking shelter at pirate ports or other shipyards that were off the grid. As Batarian ship designs were already popular with pirates, it is unknown how many of these ships were re-purposed for illegal use following the fall of the Hegemony.