We begin with our heroes at level 1, assorted motives and backgrounds leading them into business together as a classic low-rent detective agency in Sharn. Give them a random adventure or two to sort themselves out, then we get to the real business at hand; a mysterious Warforged hires them to investigate goings-on at House Cannith. Maybe a murder plot, nothing too out-of-the-ordinary. Merrix himself is a suspect (red herring), but it ultimately turns out to be some unimportant cousin who is quietly dealt with 'in house'.
At the adventure's conclusion, it is revealed that Merrix himself hired the party, explaining that the secrecy was necessary so that his involvement wouldn't taint their investigation. Impressed with their performance, he offers them a very handsome stipend to work for him full-time. Should they accept, he'll equip them with amulets that will, among nebulously-stated 'other benefits', let them communicate with him once per day.
Adventures through the heroic tier will involve investigating matters of special interest to Merrix. From the beginning it will be clear that they are in his employ, not House Cannith's, and that their work tends toward the 'black ops' end of the spectrum; not necessarily more illegal than typical adventuring, but certainly more secretive.
In the late heroic levels, the party will be sent to investigate rumours of warforged slave trafficking, with the goal of liberating the slaves (with special focus on a single slave of particular importance to Merrix). To this end, Merrix upgrades their amulets to allow them to appear to be Warforged so that they can infiltrate the slave camp and halt the operation from the inside.
(For added fun, the upgraded devices allow Merrix to observe and communicate with them as an illusion only they can see or hear, ala Al from Quantum Leap.)
In the early-to-mid paragon levels, in circumstances I haven't worked out yet, the party make a shocking discovery; they are, themselves, warforged. Their appearances are the result of embedded docents which create a specific disguise self effect. Their memories are implanted, their personalities engineered, even their bodies are specially-constructed to emulate their respective races (mechanically, I'd simply apply the Living Construct traits to their base races).
From this point, the players will either accept their role as Merrix's constructed minions or deny him, discover that his design has limited their free will, and work to subvert and ultimately escape his control.
In the case of the former, adventures will continue much as they did, though the ante will be increased appropriately for paragon-level play. Higher intrigue, more danger, etcetera. Maybe throw in some Bladerunner-style 'replicant hunters'.
In the case of the latter, it will proceed similarly, but I'll throw in opportunities for them to chip away at Merrix's control (discover an object which interferes with his observation/communications, seek out an enemy of Merrix's who could help them undo the programming that forces their loyalty, etcetera).
Whether they remain loyal or break free, the party will be drawn into the same culminating adventure in the Mournland one way or another. If loyal, they go at Merrix's behest to recover an ancient artifact from House Cannith's abandoned facilities. If they've defected, Merrix will try to appeal to their good will, or even their sense of self-preservation, by warning them that the Lord of Blades has a weapon which could destroy all of Khorvaire and must be stopped.
Over the course of the adventure the party discovers that the weapon is the doomsday device which caused the Day of Mourning. They discover that the artifact they seek is an eldritch thinking engine, unearthed on an expedition to Xen'drik, that Merrix used to calculate the remaining duration of the Last War. When it told him that the war wouldn't end for centuries, he used the doomsday device to wipe out his homeland of Cyre, thus shocking the remaining nations into peace with a mysterious atrocity he considered 'acceptable losses'.
It's revealed that he created the Lord of Blades as a red herring, his personality modeled to give him a deep hatred of the organic races, his memories altered so that he'd believe he'd been responsible for the Day of Mourning. Merrix had intended him to gather a paltry force of warforged, rise up in a doomed rebellion, and grant the nations of Khorvaire closure in destroying him (and possibly, in retaliation, every warforged in existence).
Merrix had not intended the Lord of Blades to discover the doomsday device and build it and the eldritch thinking engine (a sinister, sentient artifact of the Dael'kyr) into the body of the Becoming God, thus granting it both the power and the will to destroy all of Khorvaire.
So, by the adventure's end the party will have to brave the horrors of the Mournland, do battle with the Lord of Blades himself, and find a way to stop a Godzilla-sized Warforged with an at-will roughly on par with the Hiroshima bomb. Oh, and they'll either get to kill/expose Merrix for his crimes, or the Lord of Blades will. Either way, they're no longer his minions.
This is all a very general outline, of course. Some bits are sketchier than others. I'd love to hear your thoughts, your criticisms, your ideas, anything you might have. I like this story's potential too much to keep it to myself, so I'm sharing it while picking your brains. So!
What do you think, sirs?
That sounds awesome. Why can't you be my DM?
I think it's got something to do with that 'Location' field in the upper right corner of our posts.
It's got character options, it flows naturally toward each important plot-point with no stench of railroad, and it offers some interesting revelations.
In the early-to-mid paragon levels, in circumstances I haven't worked out yet, the party make a shocking discovery; they are, themselves, warforged. Their appearances are the result of embedded docents which create a specific disguise self effect. Their memories are implanted, their personalities engineered, even their bodies are specially-constructed to emulate their respective races (mechanically, I'd simply apply the Living Construct traits to their base races).
Glad to see the ideas bounced through in the previous thread are taking shape!
This bit is also a very interesting addition and has a lot of potential. It feels kind of a Battlestar Galactica plot (in a good way). You might even consider taking it further, in which the characters are the first model of a 'new breed' of warforged, with biological bodies but mechanical brains (Ghost in the Shell anyone?;)). They could potentially also download their consciousness into different bodies upon some circumstances - in game terms it could be seen as a resurrection or a character change or plot device like the one you have mentioned, where they need to infiltrate as mechanical warforged (at the beginning they may actually believe their new appearance is just an illusion!).
I'm aware this looks pretty much SF, but Eberron is exactly the place where fantasy crossover to SF, so to me it would be just the right place to attempt something like that