I'm sorry, this is very, VERY late, I should have posted it months ago.
Captain Sheridan was inside the artifact and Ivanova's fleet was getting its ass handed to it by the first wave of fighters. Sheridan carried the conveniently portable nuclear warhead as he floated to a stop. He started to set the bomb, attaching it firmly, when he was done he noticed a huge shadow blotting his view. He snapped around to see a cockroach straight out of hell! "Oh shit! Computer, retrace course, auto navigation, maximum burn, now!" And with that Sheridan took off, the creature in pursuit. A tentacle came from nowhere and nearly decapitated the captain. Another one moved in front of him to try and block his path. It opened the ugliest mouth he'd ever seen. Sheridan dodged to the side and flew out through the artifact's hole. He gave the signal to Ivanova and the massive Minbari/White Star fleet did what it had really wanted to do, it scrammed!
The explosion was impressive, taking out nearly all of the Third Space Creature's fighters and several alliance ships. The fleet returned and was repaired, Sheridan was picked up after his jetpack ran out of fuel. No one else could duplicate this tech yet and the artifact was destroyed, so no worries about it for now. Or are there?

Another dimension, life once flourished here, but a single malevolent race thought its genetic integrity was threatened by the mere presence of other species and therefore eradicated its neighbors. For millennia they were assured that they were all that was left in existence. Then, a large cube changed all that and they gained access to another galaxy. "The weak will perish" when you kick the Borg's ass handily, everyone worries when you say something like this. They had attempted to purge the Milky Way Galaxy of all life but a lone Federation Starship stopped them, they would no longer press an attack for fear of the nanoprobes.

What the hell do the Third Space Aliens have to do with Species 8472? Well, now it's time to find out!

The artifact, was not destroyed, the explosion damaged it but did not destroy it. It was tossed into another dimension, a realm of "fluidic space."
The entrance of the artifact sent a ripple across fluidic space, alerting Species 8472 to its presence. 7 bioships where detached to investigate. On the other side the Third Space Aliens were pissed, they had this huge fleet waiting to assault the galaxy, almost at the gate, and it's closed!! "Arg, always the luck."
The Species 8472 bioships arrive on scene. Three stay behind in a firing formation, and the remaining split into two groups to analyze the artifact. A powerful scan emitted by 2 of the bioships quickly reveals it to be an inter-dimensional portal. They also detect the remains of several aliens within the artifact. Species 8472 takes the bodies and examines them, finding them to be creatures of awesome telepathic power. The Aliens on both sides mentally probe each other to gain information. All they can grasp is a mutual feeling of malevolence, violence and hatred. There was an inexplicable urge in each to get at the other and tear into them. Species 8472 soon amassed a large fleet near the portal and began to affect repairs. A large station is built/grown and they begin to research, preparing to purge the other galaxy brought into their personal space. The Third Space Aliens managed to gain control of a few of their enemies, but never for long. Species 8472 then managed to equip their ships and other devices with shielding that would dissipate the mind powers of the Thirdies.
The Thirdies didn't know this, all they knew was that they could no longer lock onto the brains of their enemies on the other side. For nearly a month repairs were being done, and finally the big moment…

The last power cells were connected, the big moment had arrived! The portal shone with an eerie brilliance and opened. A swirl to another dimension opened and an energy shield surrounded the portal. A mad rush began 7 fighters started to come out just as 7 bioships flew in, they met roughly half way. The Thirdies were in shock as no one had ever taken the offensive against them! Two bioships poured their death weapons upon the startled ships. The shields held out several seconds before the ships popped. The Thirdies returned the favor, all 5 remaining ships spat fiery vengeance upon the bioships. The Species' vessels suffered heavy damage, one knocked off course into a spin. All bioships and fighters blasted away, with one bioship destroyed and all fighters taken down.
The six Species ships sat there to hold the position and signaled the others to follow. The two fleets collided! Dozens of fighters on both sides ran into each other just where the portal opens into Third Space.
Thirdies fired first this time, destroying half a dozen bioships in their furious attack. Species pulled back, firing all the way. They were about half way back to fluidic space when reinforcements arrived. Species pushed the Thirdies back to where the conflict started, and faced a virtual wall of Thirdie fighters. They fired and the bioships barely dodged, nearly a dozen going down. Species soon retaliated though, in a fierce series of lightning fast attacks the Thirdies were scattered and their lines had been broken. As the bioships flew into Third Space, more followed, taking out most of the fighters that remained. With little resistance for over a light year Species pushed the attack, destroying the few fighters along the way. Three fourths of the way to the nearest station, Species encountered a new threat.
A large vessel that appeared to be a barrel and shield attached to a glowing ball of purple energy blocked their way. The capital vessel was accompanied by only two fighters so Species sent 5 ships after it. The fighters concentrated their power on a bioship, destroying it, they were quickly destroyed too. The bioships fired, and to their shock and dismay, caused only moderate damage. The capital vessel turned, giving the impression it was saying "Alright, MY turn!" The ship glowed purple and a bizarre wavering beam shot forward from the main prong-thing, in its wake two bioships were destroyed and another severely damaged. The last functioning bioship dodged another blast and fired into the vessel at full power. The capital ship's shields fluctuated but held. Some thin, blue-violet beams lashed out from the globe on the back, causing cuts in the bioship. Then it destroyed the crippled bioship and moved in for the other. As it charged its forward gun the bioship laid its full power into it again, the shields were caught down as the main gun charged, both ships were destroyed.
Two more of the capital ships moved for the Species' fleet. The scout vessels were caught and torn apart by their powerful energy weapons. At the head of the fleet the Species had stopped, awaiting reinforcements. Two larger-than-normal fighters eventually came and 16 fighters were dispatched with them to assist. The capital cruisers had come with 25 of their fighters and were very confident of their chances of winning. As the Thirdies opened fire the Species dodged and formed up, the smaller ships making a circle of eight and the larger coming in the middle. The bioships pumped their power into the forward gun and they fired their planet killing rays. The fighters vaporized instantly but the capital ships shields held out for over 3 seconds before succumbing to enough power to turn a planet into gravel.
The Thirdies launched a massive offensive that pushed the Species right back into fluidic space. With incredible casualty rates mounting on both sides the Thirdies waited to launch into Species 8472's realm. The attack came and it was brutal, at the loss of 3 capital vessels and hundreds of fighters they pushed 3 Astronomical Units into fluidic space, only to be pushed back by a surge of bioships.
This bloody stalemate lasted for over 2 weeks until both sides were willing to admit that a war was getting nowhere. They then decided on the unthinkable…Negotiations!
It would be slow, but they would try to understand each other and try to settle on a peace…

8472 ambassador: "ok, why is it you destroy other civilizations?"
Third Space ambassador: "Well, they annoy us by being ugly and seeing massive destruction just gives us a nice, warm, fuzzy feeling inside."
8472: "Really? Us too!"
Third: "Plus we're much more powerful."
8472: "I'll bet! We never had anything approaching a run for our money until we met you."
Third: "Same here."
8472: "Sometimes, it gets hard though doesn't it? Even having god-like power, it is tough to battle countless other societies isn't it?"
Third: "Oh, I know where you're coming from! The planning, the massive offensives over a hundred fronts…it gives you a headache."
8472: "Yeah, sometimes…"
Third: "You could just use…"
Both: "An ally that thinks just like you do."
8472: "It will take a while, but I think I can convince my superiors we'd make an awesome team!"
Third: "Same here, I will work for it though, with the two of us combined, NOTHING will stand against us! The entire cosmos will be ash!!"
Both: "MWAHAHAHAHAHAHAHA!!!"