I would love to see a backstory mission/oro/time travel story arc where you went back in time to stop the formation of the malta.
1.You'd meet up with the people forming the malta group at "the Island of Malta" and you'd have the usual plot twists. You'd go there originally to stop them from forming. It'd be a simple mission, fight some baddies or click some glowies, maybe plant some false information or maybe just run up and beat up the forming members.
2.When you come back, you've affected history, the malta are gone, and things are better...right? Of course not. You exit the mission but it leads you back to a different mission map (not sure if this is possible?) Your contact doesn't know who you are, portal corp is shut down (the map is like the portal corp building but the lights are off/things are faded, etc.) (not sure how this would work), and there are Rikti everywhere. (You could also make the Contact that sent you now be a transformed Lost/Anaethema! How cool would that be?). Turns out that the malta were big on protecting western assets back in the day, and without 'em most of the edge of the US was lost. Without that edge, the US was weakened by the 5th Column and unprepared for the Rikti War.
You have to go around beating up some Rikti but also rescue a few Nemesis warriors that are scrounging the facility for any sources of technology that can be used for inter-dimensional travel available. You find the McGuffin (glowie), which is what they were looking for. The Nemesis folk (they should have names) are very friendly and invite you over.
3. You head over to Nemesis' place, and his area is over-run by Rikti who have taken control of the area. You start off with the two minions that you rescued (since it adds a bit of continuity, I think) and then fight, eventually rescueing Ajax(or some other known NPC), etc. and learn that the Rikti have established a firm presence on Earth, and that not many people are left. Nemesis has united with the remaining heroes and is pulling a last ditch effort to save (!?) humanity by escaping to a "wonderous new world", one where he would presumably rule.
4. You give the McGuffin to the Nemesis soldiers, enter into a Nemesis base with a big ol' portal and have to fight your way through to click it and enter... while a whole bunch of Rikti are teleporting in.
5. When you run through you are now in the Shadow Shard portal map. Lots of Nemesis are around, only these are hostile to you. You do end up rescuing one of Nemesis' men, the one you saved earlier, who tells you that Nemesis didn't even need the McGuffin that you gave him. He entered the portal before he gave it to him. You eventually get to Ajax and Nemesis in front of ANOTHER portal who are having a conversation. Nemesis says that it's installed but Ajex is talking about how he should not have left the others behind. You then fight 'em and when you beat Nemesis he confesses that someone had altered his plans, blah blah blah and that he built a time machine to go back and "fix it." So you, of course, step into the time machine.
6. You're back at the same map as #1 in the Island of Malta, only this time you have to beat up a hero dressed like you/with your powerset. You stop yourself, and then pop back to your own time.
Souvenier would be the McGuffin device. I know it's very unrefined, but I think the general idea is pretty nifty. Of course there would need to be more twists with Nemesis, but I can't think of any off the top of my head right now. Maybe you find out he was behind giving you the opportunity to time travel to Malta?