I'm running a campaign and I've hit a stumbling block, I've ended up with two of my party kidnapped, and the remaining party have killed there only lead. The remaining party do have other areas to look into though so I could put clues there, but I'd rather have those areas kept separate as there are several layers to the plot.

My preferred solution would be for the two PCs, that have been captured, to free themselves, but I'm struggling to think up a good way for them to escape that would be plausible and no rely of the incompetence of the kidnappers.

Has anyone ever had there PCs taken prisoner and how did you free them?

I'd have the kidnappers interogate the pc's and give them a chance to slip out of their bonds and escape. It'd be difficult, but possible. Barring that have the kidnappers need the pc's to do something for them, bring along a couple of guards with them and then the pc's should figure a way out.

If you are not confident in your players' ability to figure out how to escape (via Contortionist or Security Skills or just plain overpowering guards), you can give the Bad Guys a previous prisoner still held in captivity, who has devised an ingenious escape plan, but he needs help pulling it off...

Perhaps the kidnappers just want that the players run away ? There are opportunities for a variety of schemes.

Do your PC have the skills to escape on their own?

how are they being held? and how many guards?

Sounds like an excellent chance to add some terrifyingly round-corner thinking.

How clever do you want your opponents to be?

If you're thinking a machiavellian rival inquisitor with a full retinue then reliable psychic tracking, meme-implants, servo skull surveillence, callidus imposters & sleeper progamming are all possibilities.

If you're thinking single world decently organised criminals/heretics with some pull then underworld shadowing, unreliable psychic tracking, tracer devices and low grade surveillence.

If they are being held by an underground organisation then its entirly possable that the kidnappers might be subject to a raid by the local arbites or maybe even another gang. In the resulting confusion the could be freed or slip away.