Ok, quick synopsis...

PC's are investigating a psyker smuggling ring and have traced it to Planet X.

Planet X is at war with the Eldar. Their PDF is doing a great job holding them off and General Johnson is a big hero. Such a big hero that some people think he's a Saint. Inadvertantly, he's the object of veneration of a new Cult who thinks he's actually an Avatar of the Emperor (he's not...).

The actual evil Cult is behind the Gen. Johnson Cult. They're also smuggling in the psykers and infiltrating the PDF to start an army to overthrow the Planetary Governor and seize the planet.

Unbenknownst to the General, the Governor and the PC's, the Eldar have invaded for the specific purpose of wiping out the 'real' Cult, because their Farseers have predicted calamity in the future if they don't nip it in the bud and they don't trust the Imperials to clean their own house.

Now, my PC's have fought a pitched battle with the Eldar over a town where they know the Cult had a hideout. They won the battle and that's where they left off.

Meanwhile, Gen. Johnson has been assassinated. The PDF is split into 4 or 5 factions, the Eldar are still attacking, there are riots in all the major Hives and due to ineptness on the PC's part, (they didn't think to control/censor the media...) general public opinion is that the Governor with the support of the Inquisition is behind the assassination of beloved Gen. Johnson. Meanwhile the Cult is thriving. Gen. Johnson is a 'martyr', Hospitals report birth mutations up 15%, and "miracles" are becoming disturbingly common.

Imperial Guard troops are on their way, but late due to Warp storms. (They probably won't all show up...) General Shiesskopf is rallying the public and the PDF around him pointing fingers at the obviously corrupt Governor and his propped-up toadies, the Inquisition and the Ecclesiarcy. The Ecclesiarcy is in tatters as 3/4th of them are either partially or wholly immersed in the Cult and to the average Citizen, this makes the PC's and the Governorship look like Heretics, not the other way around. Gen. Shiesskopf claims the IG will surely side with him when they arrive, but secretly knows his only chance is to wipe out the Inquisition before they get here so that nobody with more authority than he has can contradict him.

Meanwhile, a group of mysterious Astartes in black armor need to show up at some point. They're part of the 'Grand Plot' and I need them to make a cameo appearance on this planet at some part.

Ok, so last we left off, the PC's won the battle and were investigating the Hideout, which consisted of an underground cistern connected by a Warehouse and a Cathedral. They found a mysterious machine which they haven't figured out yet. (It's a tech-abomination teleport device which links two machines via the Warp)

Got that? So I need 3-6 scenario ideas. I'm thinking it will culminate in a big 3 or 4-way battle, but I haven't figured out a proper catalyst for it yet. I want the catalyst to lead the adventurers off-planet. A book? Artifact? Hmmm....

Your PC are in at the machine and a tall man in very colourful cloths with a hood and silken cloth mask shows up and starts inspecting the machine. The pcs do not know what he is doing and if asked he will reply “inspecting the machine silly” in a very beautiful voice. If asked further he will tell them that he has to try and work out what is happening before these craft world bozos mess this whole situation up and weeken imperial forces in the region. And there need to be imperial forces in the region, “**** Xenophobes.” If the PC try to take the Man into custady he will say “look at that in a very ugent voice and the pc will need to make a will roll -20 not to. If any make it they will see the man drop something and the room will fill with smoke. It clears within d10 rounds and the pcs do not know where the man has gone. This is there first encounter with the Harlequin. I give him to you as I use this loon in my own game and he is much fun.if the team has any friends left and ask around he has been showing up all over the place sometimes killing elder, sometimes scaring the life out of imperials with his hideous daemon visage, always in the most random of places. The pcs get reports that he has been seen outside a temple in the Governors stronghold and go and investigate. There they do not find the Harlequin but if they go into the temple they find units loyal Gen. Shiesskopf and a rogue psyker. Battle commences. After defeat of the baddies they find they have stopped an attempt to kill the governor and retrieve the Teleport device. Was this what the harlequin was doing here? Trying to lead them to the plot?

I use the Harlequin as a very charismatic character that tends to show up in the nick of time of steers the pcs in a direction that leads to something that they need to know. He should be silly and speak like the present is the past. Have fun with him. I know I have.

I think that main question your players (and their characters) will be asking is:

Who killed the General?

If I read it correctly, General was assassinated but identity of his killer or at least identity of instigator of the killing is still unknown. Am I right?

So, they should be tracking the killer. I would do that if I was them. This kind of investigation could lead to all kinds of adventure.

Maybe even some sort of 24 in 40k...

edit: Oh, yes. Another idea:

PCs hear rumors of a brisk (cold) trade in xeno artifacts in the underhive (or something). They corner the peddlers and lo and behold it seems that someone has been supplying these thugs some generally non-world shattering eldar technology and items. But what should come as even bigger surprise to them, if they follow this lead, is that there is another acolyte cell on the planet. And Ordo Xenos one to a boot. And a radical one at that. They have been selling Eldar trinkets in order to build their own criminal network and finance their operations on a planet. Plus, they are working with Eldar. But why (I mean you already know the answer but they don't)?

Yes, I'm assuming their next course of action will be to try to find out who actually murdered the General. While I haven't actually decided who did it, I'm thinking of making it the other General who was duped by the Cult. With the planet on the brink of a Civil War, investigating this avenue in the normal fashion won't be possible, but could lead to some interesting scenarios involving gunfire and explosions.

The way I see it, the PC's have made two mistakes. One is, they didn't control the media right away. Second is, they went in guns-ablazing. Not just that, but they have about a Company's worth of Inquisitorial Guard/Stormtroopers which they landed and put into action. So, subtle investigation is probably a door closed to them. Therefore, I want to not punish them (per se) but craft some scenarios which emphasize the difficulties they've incurred by their previous actions/inactions.

Unfortunately, I've already played the Harlequin card. That was fun . Lost two PC's....heh heh. Bummer! I tried to go the RP route, but the players saw me put out the miniature and immediately started shooting. The Ninja-Clown scared the pee out of them, killed two, then vanished in a puff of smoke.

I was thinking of one scenario...

Ok, after the PC's discover the location of the Cult's base where they're keeping/training/warehousing psykers, a stealth team is sent in to place a Teleport Beacon . There's probably only 2 PC's capable of stealth, so I'm thinking the rest of them will either 1. Control the bad guys or, 2. Control one of the Grey Knights that Teleport in if the mission is successful. Although it will be a fun change of pace for my players to be able to hose everything on the board, the leaders will get away. This might be a good scenario to introduce a Flesh Hound or three or perhaps my new Juggernaut model....

Back to investigating the General, I could use a scenario or two leading up to finding the Cult base. I could just say "One of your informants hands you a dataslate..." but I'm tired of handing them info all the time.

Wait, ok, how's this?

Stealthers sneak into the Cult base with a twofold mission... Destroy the Cult Warp Teleport Device and plant a Teleport Beacon for the Grey Knights...

Of course, they haven't figured out what the Tech-Heresy device is or what it does yet....

But when they do, they could figure out where the other end(s) is and that's how they'll find the Cult Base....

If they are the button pushing type maybe they would even end up in the cults hidden lair of doom? And give them some corruption and insanity points if they do, teleporting without correct wardings can be... an experience.

Maxim C. Gatling said:

General Scheisskopf ? Really? The planet is rallying around General ****-Head? Wow. That guy must be more charismatic than the Emperor himself to get anyone to take him seriously. If General Scheisskopf has become more than just a clown, then they should pack up and fly out, they've already lost.

You have a teleportation device, and you haven't thought to have someone fall victim to it? Find a copy of the 80s remake of "The Fly" starring Jeff Goldblum and directed by David Cronenburg. Having Brundlefly crawling through the city, wreaking general mutated havoc, is good for at least one scenario.

The PC's haven't "tried it out yet"...heh heh.

Ok, the guy's real name isn't General Shiesskopf. I just couldn't remember. I have it written down at home.

Boy, I sure do hope they try out the teleporter. Would be funny if they came out the other end with extra limbs.

Knew that German GCSE would be useful.
Now, why the hell is a plent rallying around General Shithead?????!!!!!
Gah, anyway. I like the Harlequin idea, but make it so that he is clothed in rust red robes and speaks in a very badly done robotic voice.

Maxim C. Gatling said:

If they don't (some players show a disappointing amount of common sense), you can always say that someone else stumbled across the teleporter, pushed a button or three, and ended up as the new bogeyman of the hive. And, of course, all sorts of people are interested in the mutated soul, either to purge it or study it.

You could take an unexpected route and have the Ordos Xenos being the manipulators of the Eldar rather than the other way around (Farseers aren't infallible) and wanting the pointy-ears on the planet for a reason that you can come up with. The Acolytes may (or may not) do something abou this after an encounter with a random enemy (probably a cultist kill-squad, maybe an Ecclesiarchal hit-team) blows open a hole in a wall to a recently used data-mine (planning room, machine-spirit, pile of data-slates etc). This way sounds less scripted than "a big eldar did it then ran away" .

Or you could go an expected route and have them pulled up by their =][=, given hell for causing such a serious fubar and dumped elsewhere. They would then have to A) get transport, B) get back to the original area, C) pray that it hasn't all fell to pieces in their absence and D) never, ever piss off the =][= who has just beaten up all of them without breaking a sweat. This'll be both a slap on the wrist and give them time to gather info outside of their main misson area.