Here's idea #2 to leak out of my head:
[ Spoiler ]
Scavenger Hunt (or: Goo in Love)
This time, the Triads are the Johnson. They hire the runners to retrieve a family heirloom of the wife of a Triad boss (an ornate jar of lotion believed to date from some ancient dynasty or another -- hit wikipedia to be more specific). The triads believe that it was stolen by the DIMR, who have been hanging around constantly for the past six months trying to negotiate for the item.
The triads believe that the DIMR has taken it to a smaller facility in the barrens for some preliminary research before it is moved to the more secure facility. The Triads want the runners to return the heirloom (undamaged of course!), but they need plausible deniability to avoid starting open hostilities with the DIMR.
Assuming the runners can break in to the DIMR research office (no doubt guarded by a wide assortment of technological and magical means -- though some of those may be for keeping things in as well as out), they will find that the DIMR doesn't have the item either. Since their pay is based on returning the lotion bottle, not breaking in, hopefully they will use this opportunity to search the facility's computers for what info the DIMR does have.
What they find is what they (probably) suspect; the heirloom is some sort of magical artifact. All the DIMR knows is that the Triads have lost it, and a few scattered notes about it possibly being in the possession of one Ren Yum, an ork Triad.
At this point, the runners will need to hit up their contacts to try to find information. What they should eventually learn is that Ren Yum had the distasteful job of keeping a large clan of ghouls out of the Triad's business. Unfortunately for Ren, the ghouls have actually begun to negotiate for a cease fire, and he is in the unenviable position of negotiating with them regularly. The runners should be able to track down, either from contacts or ghoul attack reports, the rough location of the ghoul clan's home base -- an abandoned geothermal plant deep underground that connects to a number of interesting locations via some abandoned subway tunnels and the ork underground (which is how Ren has been going to see them.)
If the runners have contacts in the Ork Underground, they will get information that Ren has been acting very strange, that he somehow managed to recruit some orks from the underground to help him, and that there are reports something "major" happened between him and the ghouls last time they met. He (and his recruits) haven't been seen since.
Whether the runners get the information from the orks or not, the runners (after a few various encounters in the sewer/subway tunnels -- devil rats, sewer people, a toxic spirit, or whatever strikes your fancy) make their way to the geothermal plant's control room. There they find massive carnage -- dead orks and ghouls everywhere. Also, there are a half-dozen not-quite-dead ghouls who attack the runners.
The runners can negotiate with the ghouls -- they simply mistakenly believe they are Ren's men come to finish the job they started. Ren had attacked the ghouls under a flag of truce, and slaughtered the ones at the meeting. A few wounded ones were left behind, and a few of their clansmen had returned just as the runners did. Should the runners negotiate successfully, or subdue the ghouls without killing them and then interrogate them, they will get further information (at this point the ghouls have little to loose, so will not be difficult to interrogate)
The ghouls will inform the runners that Ren showed up carrying the heirloom that they are seeking -- and that the heirloom was indeed magical in nature. What the ghouls know that the DIMR does not is that the heirloom is a phylactery for a very ancient free spirit. The spirit's nature is a gooey substance that is concealed in the jar, resembling lotion. (An inhabitation gone bad?) The spirit has compulsion and mind control powers and spells, and the ghouls recognized its effects on Ren and the orks he had brought immediately because of their astral nature. As soon as Ren realized the secret was out, they attacked the ghouls, and the carnage the runners see ensued.
What Ren was after from the ghouls was information regarding a peculiar magical waxy substance they found in the steam tunnels. The ghouls had sold it for what they thought was a startlingly high price to one Victor Krastov. Victor is a troll violinist, and a world famous one at that. The ghouls have a few fliers for Victor's next concert (in two days) on them -- and this is all the runners will find if they kill all the ghouls. It's up to them in that case to continue the scavenger hunt with so little information.
If the runners try to find Ren and his band (which now includes both the surviving orks and a few ghouls, all under the influence of the free spirit) they can mange to track a few stragglers and new additions (mostly street bums) from various strange police and street level reports. Ren himself remains elusive however.
The concert is put on with Sara Tuy, a beautiful female elven vocalist. While Sara is quite skillful, it is Victor's performances that the critics have been raving about. What the critics, and likely the runners don't know is that Victor owes the Triads a good deal of money. The Triads have some body guards at Victor's performance (only two) because of this. The body guards know nothing about the missing heirloom or the runners, however.
During the concert, Ren's band of mind-controlled orks and ghouls (along with Ren himself, now deep under the control of the gooey free spirit) attack the concert. Some spirits summoned by one of the ghouls (a rat shaman) and some explosives that collapse the lobby seal the concert hall, trapping a room full of panicked hostages and the runners (if they attended) inside.
Ren takes an immediate interest in Victor. What he will attempt to do is grab Victor's violin (over the objections of his bodyguards), and Sara (if Sara escapes with the help of the runners, or if Victor is driven off, he'll grab anyone at random from the audience.) Ren will perform a very quick sacrifice ritual (Ren is a street sam, but is being driven by the goo spirit) -- and the result of this sacrifice is the goo spirit's goal.
Unbeknownst to the runners, Triads, Ren, or anyone but the goo spirit, Victor's violin wax -- the mysterious substance he bought from the ghouls, and incidentally the cause of his incredible abilities -- is also a free spirit that has been lying dormant in the underground tunnels of the geothermal plant. The sacrifice ritual will reawaken this second goo spirit -- who turns out to be the first spirit's lover!
There are a lot of possibilities for how this final scene goes down, depending on the runners. They may try to intervene and drive Victor off, in which case he will try to escape "backstage" or into the catwalks or somewhere else equally likely to loose the runners for long enough to find a victim and sacrifice them (this is the goo spirit's only real objective.) He will do this while the rest of his mind controlled band hold off the runners. The goo spirit also is providing Ren with magical protection, in the form of both counterspelling and an armor spell (or possibly even some variant on possession that gives Ren the bonuses of possession, but the goo spirit's physical form remains -- though dormant.) Also, the sacrifice ritual happens pretty quickly (a few actions to draw a circle, then just a quick spur attack by Ren), so the runners may be caught by surprise. Lastly, its possible that with the information from the ghouls, the runners will confront Victor. Because he doesn't want to loose his newfound fame, let alone find himself unable to pay back the Triads, he won't be very cooperative. His bodyguards will take his side, unless the runners are very convincing about their Triad employers and the importance of their assignment. If forced by violence (or a believable threat of it that would overwhelm his bodyguards) he may turn over the wax -- but when that happens, Ren will attack the concert hall regardless. The runners may then find themselves holding the gooey body of the second spirit, as the sacrifice ritual only requires line of sight to the wax.
How things go down after the second goo spirit is awakened depend greatly on the runners and their actions so far. The spirits will try to escape, and care nothing for Ren and the others (who were just tools in their drive to be reunited.) However, if the runners were sufficiently antagonistic, or are sufficiently determined to retrieve the lotion bottle (which the spirits must take with them, as it binds up the life force of the first spirit) they will fight. The second spirit has powers very different from the first (which works mostly through manipulation), the GM should pick a theme of powers that would interest and challenge the runners.
In the end, the runners have several things they can be rewarded for or punished for:
1) If they manage to purge or bind the spirit in the lotion bottle, and return it to the Triads(their original objective)
2) They could loose points if Victor is harmed, because he would be unable to repay the Triads.
3) If the runners find a way for Victor to pay back the Triads somehow (because without the wax, he won't be able to play well enough to earn the money for a long time) the Triads will cut them in on the payback.
4) If the runners patch things up with the ghouls, who currently believe the Triads are at war with them (because Ren was their official envoy) the Triads will be greatful for their initiative. (They may also hire the runners to do this if they don't do it on their own, though the pay would be less.)
5) Anything interesting they manage to snag while in the DIMR research center (unless the DIMR catches them of course!)
6) The "eternal gratitude" of the beautiful and talented Sara, whose career doesn't depend on magic wax, should the runners save her in a particularly dramatic fashion (which is always good for publicity!)
7) There's a lot of potential for notoriety in this final scene, because there are so many potential hostages and bystanders in the theater.
The general theme of the first part of the run is a "scavenger hunt, shadowrun style" feel. The runners continually fight, sneak, and scheme their way past obstacle after obstacle, only to be lead to a totally new objective.
The last part of the run should emphasize the pandemonium of a trapped, panicked crowd, and the alien and uncaring nature of the spirits. It should also have some visual effect emphasizing the love of the spirits once they are finally reunited. This will help drive home that in the confusing and dystopian world of shadowrun, even love can bring chaos and death.