How big an adventure do you want this to be?
There's a skeleton (so to speak) coming together in my head, but it may be more than you want.
It also makes heavy use of the 4E book Open Grave, which may not be to your taste.
St Vargas skinned the dragon and cast it back into the water: the various bits of the dragon have animated in different ways.
The dragon's skull serves as a reskinned brain in a jar: the dragon's bones have become crawling claws or crawling gauntlets. Bits of the dragon's flesh have become tomb motes.
The dragon wishes to reclaim the armor of St Vargas, which is made from his skin.
If he get his animated skull, bones, and flesh into the armor, he will be reborn. (Probably as some kind of blasphemous evil undead dragon, but he may not know that or may not care: he's been split apart for what, 200 years? He's desperate.)
But the dragon is undead, not stupid. He recognizes he can't just float into town with a flock of animated flesh in tow. He needs agents.
He has been working with a clutch of kobolds: their exposure to the necrotic energies of the dragon's undead carcass has rendered some of them Tomb Tainted. Their leatherworking skills have allowed him to try and create agents.
When the bits of dragon and the kobolds capture someone and flay them alive, the flayed skin becomes a forsaken shell. This shell has the power to envelop someone and control their bodies: like a sock puppet that controls the hand inside.
The forsaken shells are then convinced (not easily or always successfully) to try and envelop dogsbodies who can walk them into the museum, take the armor, and then return to the dragon bearing it.
Due to various combinations of racial incompatibility, treacherous forsaken shell agents, and the weakness of low-level pilgrims that die before they can be walked to the town the dragon has not yet recovered his skin.
All he has done is create a quantity of forsaken shells with varying degrees of commitment to his mission. The forsaken shells have started preying on the pilgrim traffic with such success it's caused PC attracting worthy alarm.
One of the pilgrims whose skin was animated was a person who has a perfect right to enter the museum and remove articles: perhaps a noble representative of the church empowered to place this holy relic in a chapel instead of a secular location.
The average pilgrim doesn't last very long when he gets enveloped. But if this noble forsaken shell can envelop someone with more hit points...say, a PC...the host might last long enough to enter the museum and get out.
The PC's must close the kobold tannery and kill all the dragon bits, all the while being stalked by the noble forsaken shell. The shell doesn't want to fight the PC's, but will negotiate with the party once it has someone enveloped. All they'll have to do is come along and help the forsaken shell steal the armor: then their friend will be let go.
Will the party be captured by the kobolds and fed to the forsaken shell?
Will the forsaken shell (and the dragon bits) keep their word once the party helps them recover the armor?
Will the party kill the dragon, or does the dragon come back?
