As you are probably aware, there was supposed to be a film called Stargate: Extinction. Then cancelled, then maybe revived and so forth.
Let us stick to the idea of extinction. Now, we can add brand new enemies, but let us keep low profile. Who is threatened with extincion by the end of SG Atlantis? The Asgard race in Ida is gone and all that remains are their cousins in Pegasus. The lost tribe. We know they are hiding on a planet with toxic atmosphere but are running out of time. Since their failed attempt to use the Attero device to destroy the wraith, they are in desperate need of aid.
So, let us imagine that the Wraith have found the Asgard last bastion. Let us call this planet Bastus. Why would the Wraith seek to wipe them out? Because they see them as a potential enemy. Because they have something the Wraith need. Energy generation technology. As mentioned by Rodney, that is the Achilles heel of their technology. The more energy, the bigger and stronger hive ships they can grow. And thus they will not give up this grand prize. Asgard, desperate to survive, send out a signal. Call for aid. Atlantis, as a city-ship formerly belonging to their allies, the Ancients, will catch this signal. And so the race to save the Asgard begins. At first, only one hive ship and small escort fleet is besieging the planet Bastus. But as soon as the Tau´ri intervene, this conflict starts to grow. Until, ultimately, the whole Wraith race bonds together once again. And so the War of Extinction begins. Only one can survive. The Asgard or the Wraith race will die. Or so it seems. As the war progresses, moral question begins to rise. Do we (Tau´ri or Wraith) have the right to wipe out an entire race? The Asgard have very advanced cloning program. Maybe making clones the wraith can feed on? As this idea begins to gain root, Tedd will join forces with Asgard and Tau´ri to try and create a prototype hive-ship. One capable of growing clones to feed its crew. But not everyone is comfortable with this idea. Subfactions on both the Wraith and Tau´ri side prefer total annihilation rather than coexistence and cooperation. And so you have to fight renegades and enemies, pirates and natives, to accomplish your goal. And maybe, just maybe, there is someone else out there, who also got the Asgard call for aid. Like the long lost Furling race, or the secretive and stealthy Nox.
Alright, I will write down here in the first post the story that I have, only from the tau´ri perspective tho, to keep it short. Check for future edits!
The story so far:
A strange signal is received at the Atlantis HQ. Atlantis computer pinpoints the source. It is a planet with atmosphere full of gases and no life-forms are known to be present on the surface. An SG team is sent in a jumper to investigate. A 304 drops them only a short jump away, waiting for the team to investigate in a jumper. That´s where the campaign begins. Jumper enters the system, dialogue about the mission and some asgard tech detected on surface, order to approach stealthily to investigate. Wraith hive ship immediately detected entering the planet´s orbit. After the stealthed jumper approaches a battle is witnessed between the vanir and wraith. Vanir get blown up so the nearby 304 enters the battle (should be a hero ship). When the day is won contact with Vanir is established. They are very distrustful of us, remembering how we sabotaged their plan to blow up all the stargates and wraith ships with Attero device. Thus our task is clear. Gain their trust while keeping the wraith away. Couple of hit and runs on wraith fleets and shipyards in the vicinity should take care of the wraith, although they will eventually come to see what all the fuss is about. The asgard situation is complicated since it is absolutely critical that they manage to save their cloning research and cloning facilities, otherwise they will meet the fate of Othala Asgard. Stargate overseers also are not that happy with us risking all-out war with the wraith. Yet if the wraith get their hands on asgard energy generation tech, they will wipe the galaxy clean in a matter of months. And so, amidst all the enemies (wraith mobilising into a giant fleet to attack the Vanir, Goa´uld remnants appearing (tho since the goa´uld numbers got a pretty big hit, they will act more like Tyber Zann in the original FoC) and natives getting riled up, order comes up to either move the asgard now or blow up the whole planet and run away, ensuring that the wraith will not get their hands on the asgard tech at all costs while also avoiding an all-out war. At this moment Tedd gives us a call, askin to get his claws on the asgard cloning research, promising that letting the wraith grow up their own food will ensure lasting peace (and his dominion over all wraith). What will we do? Do we join Tedd, one of the wraith or do we follow orders? There is no real guarantee that Tedd will be able to control all the wraith nor that he will actually not send them our way after hes the big boss. And if we give the wraith their own means of producing sustenance, what will stop them from conquering everything in their way? If we stand our ground, it will be either the Vanir or the Wraith. One will have to die for the other to live. If we run, the asgard are done for. If we cooperate with Tedd, we may start the greatest wraith conquest since the first contact war between the Wraith and the Ancients. All the while an unknown force speeds towards us, unknown whether friend or foe.