So the team is investigating a case involving a serial killer, and the evidence seems to point to this cult leader. The case gets closed down quickly, the cult leader goes to prison thanks to the team’s testimony, and the team figures they’re done.
But then, some days or weeks later, Hotch and Reid are chatting as they head through the parking garage, when suddenly boom! they get jumped by a bunch of cultists. They subdue our heroes without any significant fight, through either the threat of tasers, or the use of physical force (there's at least half a dozen of these guys).
Only, these are the nicest, most apologetic and solicitous cultist kidnappers you've ever seen! They're super careful to avoid inadvertent harm. After they've disarmed our heroes, one of the cultists pulls out a little kit with knockout drugs, and says they're going to take Reid, but they don't want to hurt him, and does he have any allergies because they'd feel really bad if anything happened. Hotch and Reid try to persuade them not to do this -- all the many reasons it's a bad idea -- but they're firm about this. They say they tried to make their voices known before their leader went to prison, but nobody listened, and now they're hoping that this incentive will get the team to re-examine the evidence.
Reid says that he's allergic to [common knock-out medication], so they choose a different one. Meanwhile, other cultists tie up Hotch (or possibly knock him out) and leave him in a safe place where he's going to be easily found, with a note. Then they carefully sedate Reid, who's scared but doesn't have much choice but to passively accept this; and they're still apologizing while they're doing it. They get him into the back seat of their car/van, between two cultists, and pretty soon he's passed out.
Reid wakes up in a secluded mountain cabin, a place the team hadn't found and certainly hadn't connected to the cultists. He has no idea where he is (though he might make some inferences due to the details). He's quite troubled and somewhat afraid, but these guys aren't the least bit threatening -- aside from the fact that he's not allowed to leave yet. Some of them sit him down to discuss the situation, now that they've definitely got the team's attention. Basically, their testimony about their leader was discounted and there's no possible way that he could be the killer that the team assumed he was, etc. etc. They only kidnapped him because they were desperate and nobody was listening; maybe the team will now have the motivation to investigate the case more thoroughly. Certainly they don't want the actual killer to be running around free.
So Reid starts actually paying attention to the details of this group, and comes to the conclusion that there's something very off about this: He could see a guy as violent as the killer attracting a group of people this devoted, and he could see the guy's charisma attracting a group of somewhat deluded pacifists, but he can't see the combination for this particular case. These guys don't fit the profile of the cultists that the serial killer would've attracted.
One of the cultists is tech-savvy enough to provide a way for Reid to contact his team but not be immediately traced back to them, and Reid is allowed to have some uncensored time talking with the group. He points out that these guys are certainly desperate, but they're not violent, and he's seen no hint of weaponry or poison or anything the team would have to be careful of once they track the place down. And he hopes it's not just the Stockholm Syndrome talking, but he'd like the team to look into the case again, because it's pretty clear at this point that they seriously missed something. Not that he wants them to stop looking for him -- he certainly doesn't want to stay captive -- but re-examine the case.
Within a few days, the cultists get Reid into the car and drive him out to a city center and drop him off in a safe location, maybe after buying him a new phone. And the case proceeds. There's consequences for the cultist kidnappers, of course, some sort of consequences, but it does turn out that their leader is not the serial killer, and the team manages to track down the real killer before too long. Luckily just in time! or whatever.
So, that's the general idea -- and if anyone wants to pick up this idea and run with it, have at it! I'm never stingy with my ideas.