Well, just to offer an example from my own arcs, not at all definitive: my Neutral arc involves helping the University bug-test their AE Arc. The only opponents are simulated, and the character is renumerated for their assistance. I leave it ambiguous whether it's Paragon or Aeon U that's involved, too. I'm sure the same troubleshooter role could be applied to more dramatic arcs - research firm offers massive moolah to get rare samples from territory infested with monsters, or whatever. No crime-fighting or -committing involved, just rewards for involvement.
"Neutral" is a much broader category than "heroic" or "villainous," though it can take more creativity. Since you said you wanted to avoid the alien threat situation, how about a few of the following?
For low-level players, a science team goes out of contact. Villains and heroes are hired to bring an agent to their last location. As the arc develops, a small-time mastermind takes personal enmity to the task force.
For mid-level players, a religious figure calls for a meeting between two enemies for a peaceful exchange of some kind. When the meeting location is reached, however, the villain ambushes the figure and his escort. There's some very specific dialogue I could think of here, but I won't get that detailed. However, as the arc progresses the task force learns that the figure is the organizer and they take him down based on their own motivations (probably leaning towards revenge or justice).
I won't really get into high-level arcs, as there are way too many ideas. Of course, these two could be made to fit just about any range. Really, you could do just about anything. It is a simulator, after all, and what villains call villainy could be construed as research for a hero. Likewise, a villain might get a kick out of rescuing holo civvies after firebombing much of Paragon City in the "real world."
Ok so your villain isn't interested in preventing villainy, and your hero isn't interested in getting paid. It sounds to me like the "preventing villainy" motivation is in place for the hero, and the "getting paid" is for the villain.
It is entirely possible to have an arc for both villains and heroes, without forcing villains into heroics to save the world (which is, after all, where they keep all their stuff). The easy way is to have an arc where you stop the bad guys, but there is the potential for profit, either a contact who offers to pay you or mission objectives consisting of, for example cool stuff you can either give back to the proper owners or keep for yourself, hostages you can set free or hold for ransom, etc.
Aside from that, there are "investigation" type arcs, where the motivation is curiosity. Humorous arcs can transcend morality. Arcs involving "co-op" groups, such as the Vanguard, the Midnight Squad, and Cimerora can easily be made neutral, although in many cases it would be villains playing hero. There are also the "grey" morality arcs, which are designed to be suitable for an anti-hero or anti-villain (and should probably be labelled as such, to avoid comments along the lines of "Heroes don't kill")
Eva Destruction AR/Fire/Munitions Blaster
Darkfire Avenger DM/SD/Body Scrapper
Arc ID#161629 Freaks, Geeks, and Men in Black
Arc ID#431270 Until the End of the World
I usually stick to Heroic arcs for my Heroes and Villainous arcs for my Villains.
I'm currently playing a Neutral arc with a hero, and the contact is treating me pretty badly. He's asking me to do stuff and promising that he'll 'owe' me something for it. The objectives are all in his business interests, so his motivation is clear, and the stuff I'm doing is against villains, so my hero isnt being forced to do villainous things.
The problem as I see it is that if i was a villain, I'm not sure I'd be interested in preventing the villainy, and my hero isnt interested in being a paid stooge of some business guy. There's no real reason for either of them to listen to the contact.
What do you think 'Neutral' is for? Is it for arcs that can be played without problem by Heroes or Villains, or is it rather the closest we have to a 'mercenary' morality? Is it even possible to write an arc that both heroes and Villains can play without resorting to the old 'alien threatens whole planet' routine?
Eco.
MArcs:
The Echo, Arc ID 1688 (5mish, easy, drama)
The Audition, Arc ID 221240 (6 mish, complex mech, comedy)
Storming Citadel, Arc ID 379488 (lowbie, 1mish, 10-min timed)