These are a couple ideas I have been playing around with for campaigns / long stories. Many of these involve reversals of characters' perspective about their opponents.
1) The healer -- The foreground of this campaign, initially, is a conflict with slavers who have been operating in the area (assumed to be Theran). Over the course of the campaign, however, the background / subplots begin to take over the and merge with the foreground. This campaign revolves around an ally of the PCs: a high circle patron and questor of Garlen who steps forward to reward the PCs for good deeds to innocents who cannot pay for the service (i.e. peasants), and who provides healing, shelter, and understanding when the heroes are in need. In the beginning, she should be a 100% sympathetic character, albeit with the evangelical quality common to many questors. Her attempts at conversion / persuasion are gentle enough at the start, though, so the PCs should have little reason to object.
The healer is a high-circle human archmage (a magus who is versatile in all the spellcasting disciplines). She specializes in healing magic, and in the necromantic and controlling sides of Nethermancy and Illusion. She is a vegetarian (vegan), a pacifist, and a mother hen. She truly does care about her charges, and want to keep them close and sheltered from all life's woes. She is a strong pacifist, who beleives that even the worst offenders can be redeemed, and can lead productive lives. In return for reduced prices on healing goods, and other services, she tries to convince the PCs of the inherent worth of all life. "Where there is life, there is hope." is almost a mantra for her. She attempts to convince the characters to use lassoes and whips, attacks to stun and knock down, negotiation and other non-lethal, non-harmful means to oppose the injustice of the world. She encourages them to "Avoid rather than Defend, Defend rather than Control, Control rather than Oppose, Oppose rather than Harm, Harm rather than Maim, Maim rather than Kill." She also encourages the PCs to bring their opponents to her, so that she may help in redeeming them and showing them the error of their ways. She sincerely intends to keep them doing further harm, and her ability (and the gratitude of those she has helped before) are more than sufficient for this cause.
The healer, however, has follwed her ideals down a dark path. Such a high-circle follower of Garlen was too great a temptation to resist, and so the Mad passions have combined their talents toward her corruption. Raggok has fueled her anger at the injustice of Death. He has convinced her of the righteousness of the Rulership of her ideals over others lives. Most significanlty, he has given her the power to best death: to create the undead. After all, no matter how much pain they endure, according to her philosophy, even maiming is preferrable to death. Dis has fostered her belief that she can save everyone, encouraged her to see one way as the best and only way. Moreover, he has granted her the ability to "show them the One True Way" by forcing obedience to her personal ideals. Most insidious of all these is Vestrial: the Clown has hidden from her the effects of what she is doing. So long as she preserves the body, she is blind to the pain of the spirit. It is, in fact, the healer who employs the slavers: she is gathering in her flock so that they can be close to her, protected by the shelter of her hearth (more on this below).
Whether or not she is redeemable or is corrupted beyond redemption up to the PCs and how they approach her. Whatever the case, they will eventually wish to confront her in her lair: a necropolis / kaer whose inhabitants she "saved" from the Scourge, and whose loyalty she commands both as the local hero, and through the assistance of her spells. A great many of the kaer's residents do not even realize that they are dead, and attribute their emotional / spiritual torment to their own weakness. After all, their spirits are always lifted (or rather, their depression is magically suppressed) when they are in the healer's presence.
2) The summoner -- This campaign is not entirely well-suited to Earthdawn, as the main antagonist possesses magic that is less common id ED than in other fantasy games: summoning. He has the ability to magically transport animals, namegivers, and spirits to his location and magically compel them to do his bidding. The summoned creatures are not mindless automatons, and frequently harbor a grudge, but the mage holds a magical advantage in the ability to compel obedience to at least the letter, if not the spirit, of his commands.
The conflict arises when the mage (covertly, but clues and opportunities to sabotage his plans should be present) obtains the links and components needed to summon the PCs. The mage is an enchanter, and he is well aware that he will likely obtain better results by persuasion than compulsion, so he attempts to be reasonable and personable to the characters, and will attempt to strike bargains with them rather than compel them. In fact, they may wind up working for him willingly the first few times he summons them, unless they are particularly contrary or were called away from something particularly important. In fact, the summoner is not entirely opposed to sending them back if he has others who could serve him and the summons is particularly inconvenient for the party. In general, the party should probably be initially annoyed, but the summoner should be played in a sufficiently noble and ingratiating manner than the party is at most annoyed by him, not hot for his blood.
Unfortunately, destiny is not on the side of our summoner, and in his quest, he manages to break some of his toys. Saddened as he is by this loss, he is certain that his cause is just, and that they would have given their lives willingly if only they had understood (and there is something of the "they were only summoned creatures anyway" mentality as well). But, as his options for other helpers dwindle, he is forced to rely more and more on the PCs services. Where before the tasks may have been easy or agreeable, he begins to be forced to use them for more dangerous or onerous tasks ("Cover my retreat!").
Complications, once the PCs decide they want this man's blood (or at least to give him a stern talking-to while the tables are turned), are many. He moves around a great deal. Further, he is well aware of the power knowledge gives over a pattern, so he is careful during each of his summonings to be pleasant and inquisitive, but to always wear a mask (magical or otherwise) and never to reveal more than he has to. The PCs are forced to piece together his purpose from the evidence of the tasks they are required to perform.
Whther the PCs ultimately decide that his purpose is just or not, or whether it justifies his actions, is up to them, but do your best to make it a hard choice. The summoner should be on a quest of monumental importance (he is high enough circle to summon the PCs, and to pose them a significant risk in a fair fight), and that quest should have far-reaching (positive) consequences. On the other hand, it would not hurt him at all to be reminded that no matter how noble his cause, his victims are real people with real lives, and real families who greive for them when they misteriously disappear, and then reappear dead, without ever an explanation, without knowing what they were dying for, and without ever a chance to say goodbye.
The PCs should have a chance to meet some of these families in the process of tracking down the summoner, most likely because they were summoned at the same time as another adept, who was less deceptive than the summoner himself. By piecing together what all the summoners victims have in common, and adding that to the subjects he asks them to research, the opponents he asks them to fight, etc., the PCs eventually gather enough knowledge to anticipate his whereabouts and confront him directly.
A couple final notes: First, don't get caught in the trap of only summoning the PCs for combat purposes. Just think how many uses your very own personal (and portable!) menagerie could have: entertainers, researchers, laborers, etc. One possible scenario involves the PCs being sold into slavery by the summoner... this allows him to infiltrate the slavers, get what he needs, and PRESTO! the PCs are returned home by the ending of the summoning magic. No guilt pangs over leaving some poor name-givers in slavery.
Second, this campaign was inspired in large part by my frustration with the problems of players not being able to make all the gaming sessions. Some people simply ignore the "disappearing / reappearing PC" problem, but it has always bothered me. Still, it bothered me even more when we couldn't game for months at a time because first one person and then another had schedule conflicts. OK, cutting to the chase (and ending the rant, sorry about that): part of the point was that missing players were summoned away at inopportune moments. They were gone as long as needed, but on their return, they would be responsible for creating some entertaining story of exactly what use the summoner had put them to (with some GM guidance to prevent the summoner's personality and goals from being totally warped).