I think I've decided to go with a variation on Noble Drake's suggestions. Here's what I've got so far. Feel free to critique or make suggestions...
First things first, it's pitch black down here. Seemed like a good idea to take advantage of my team's complete lack of light source. Everyone has low-light vision, but nothing that will help them in absolute dark. If they ask about having something that will help, I'll suggest they use their commlink's dimly lit screen. Once they get moving they'll discover a backpack in the middle of the tunnel with some odds and ends inside including a commlink and some flares. If they check the device (before the battery dies), they'll find an email on it from a company called NuYu, thanking the recipient for inquiring about their augmentation exchange program and suggesting he stop by one of their several Seattle locations. There's also going to be pictures of a young couple on the commlink as well as several unanswered outgoing calls to someone named Chloe. If they strike up the flares, they'll notice that the backpack was in a puddle and that there's a smear leading away from the bag and around the corner.
From there, the team will round a corner and stumble onto some four-legged animals eating something off the ground. I'm undecided just what these animals are, but I'm leaning toward either your garden variety dogs, or something a bit more intense like a pair of hellhounds or devilrats. If the team lit up the flares, they'll be immediately noticed, but if not I'll give them the chance to sneak past. Ultimately, the dogs will be eating the remains of the backpack owner who appears to be the same man in the commlink image. I'll have a flier for NuYu in his pocket, just in case they blow it with the commlink and decide to search the man instead.
At the end of this segment of the tunnel they'll come to a junction. If they go left, they'll come upon an out of place security door which will lead to that operation room. If they go right, however, they'll notice that the sewer tunnel pitches steeply downward. As they proceed, they'll eventually come to a man with his back to them. This man, in bloody scrubs, is bending over, picking bundles up, and tossing them over a large drop-off. If confronted, he'll try and play it cool when he sees that he's outnumbered, but will eventually try and get the drop on them. If the team investigates the drop off and the bundles, they'll find the man has been tossing human body parts down into a deep chasm. If they find a way to illuminate the bottom (maybe with one of those flares), they'll see those ghouls that Noble Drake suggested. Once they decide how to deal with this man, they'll eventually have to head back to the junction and inside the room.
Once they're in there, they're going to see all sorts of budget medical supplies and equipment, as well as a series of used cyberware parts (several still wet with blood). In the middle of the room they'll see a sheet covered table with a human shape beneath it. If checked, the sheet is covering a woman (the same woman in the commlink pictures, Chloe Whidmore). I'm considering having her still alive and having her awaken with a scream. If she awakens, she'll explain what she was doing there and who the man they found dumping body parts was. (thus explaining NuYu)
If they team searches the room they'll find a staircase behind a door leading them out of the sewer and into a shoddy looking makeshift storefront for NuYu. It's the middle of the night, so they won't have any security issues, but they'll need to turn the alarm off before they can leave the building.
From there, I'll plant the seed that they need to get their van back (left a couple of blocks away from the pawn shop), but I might mention that, at this point, there's probably a LOT more Lone Star on the scene (might make someone roll for that info). However, the part of town they're in right now is the infamous Gang Row, and they're going to have to hoof it into a better section of the area if they want to try and call for a cab or something comparable.
Either way, they'll be making some sneak rolls and possibly either fighting gangs or mob/lonestar. Once this is resolved, they'll be notifying the NPC with the lonestar contact about the double-cross and either dealing with that or wrapping it up.
Thoughts?