I'm considering picking up Dark Heresy 2nd edition when it's released and GM a campaign. I've DMed D&D extensively, but I'm keen on something else. I'm somewhat familiar with the crunch and I'm quite familiar with the WH40K fluff, but I've run into a slight snag.

Session 1:

I'm gonna start the campaign off with the pen and paper RPG equivalent to an opening cinematic: an Ordo Xenos Inquisitor, Tiberius, along with a few Deathwatch Space Marines, have been dispatched to investigate a possible alien artefact-worshipping cult on a Hive World. As they leave the space port one Deathwatch Space Marine, Alcaeus, is sent to scout, and Tiberius' party is ambushed well-equipped and well-informed cultists, leaving Tiberius wounded and all his accompanying Deathwatch dead. Alcaeus returns in a cascade of bolter fire and krak grenades, rescuing Tiberius by dragging him into the nearest building, a barracks.

The PCs are in the barracks, and will now by Inquisitorial Edict be conscripted into the Inquisition. The players are then going to have try to get the wounded Inquisitor to safety with the help from Alcaeus

Session 2:

Here they're sent by the Inquisitor to find out what they can about the cult. A small fight and interrogation of surviving cultists. Alcaeus and Tiberius stay away as to not arouse suspicion.

Session 3:

Showdown with the cultists, only to find out the artefact they're worshipping was brought by a red-armoured Space Marine calling himself the Bearer of the Word. They learn he's not on the planet anymore, but find out that the ship he left on went to a Feral Planet inhabited by techno-barbarians.

Session 4:

Pursue the Word Bearer to the Feral World and have some Mad Max-style fun tracking him down.

Plot Twist #1:
It was the

a) Alpha Legion

or

b) Ghosts of a Eris, a homebrew Alpha Legion successor chapter masquerading as loyalists

who let the Inquisition know about the cult.

Plot Twist #2:
The surviving Deathwatch Space Marine is infiltrating the Inquisition and planned the ambush in an attempt to build trust between him and the Inquisitor. He is actually

a) an Alpha Legionnaire who has literally transplanted the previous marine's face onto his own
or
b) a Ghost of Eris who has literally transplanted the previous marine's face onto his own.

The Alpha Legion/Ghosts of Eris are infiltrating the Inquisition to try to turn Tiberius into a Hydra operative (Potentially with psycho-indoctrination), or if that fails, to replace him with an Alpha Legionnaire/Ghost of Eris.

Plot Twist #3:

Unbeknownst to everyone, the Alpha Legion/Ghosts of Eris are actually rooting out the Word Bearer cult due to

a) they don't want the planet to fall to the Word Bearers

or if Alpha Legion

b) they want to take over the cult

c) the cult is in direct competition with one of their own cults

or if Ghosts of Eris

d) they want an uncorrupted planet to recruit from, so to arouse the least amount of suspicion.

Alcaeus also has special Alpha Legion equipment - specifically disguise equipment to allow himself to appear as a normal human. This equipment was used by Efritt squads previously (see the Primarch short stories).

In summary, the PCs will be doing the Alpha Legion's dirty work. If they eventually learn they're being duped it might be too late for them and they'll already be branded heretics, or it might be early enough to foil the Alpha Legion/Ghosts of Eris' plans, and maybe even expose them, or at the very least prove their own innocence (not that it'll count for much). Hell, they might even join the Alpha Legion or Ghosts of Eris to potentially become Space Marines, or convince Tiberius that the only way out is Exterminatus.

Potential ideas:
The alien artefact is a necron artefact (this has been done to death though).

The alien artefact is an Eldar artefact.

The alient artefact is a Chaos artefact.

The Feral World harbours many dark Chaos beasts (Mad Max, meet Riddick).

The Alpha Legion/Ghosts of Eris try psycho-indoctrinating the PCs.

The Snag(s):

The snag is I'd rather have them work with the Ordo Hereticus, but that blows the Deathwatch out of the plot. Any ideas how to circumvent that and what sounds more fun, the Alpha Legion or the Ghosts of Eris? Also, any thoughts or potential ideas?

Hydra Dominatus.

anyone?

anyone?

Why do you want them to work for the Ordo Hereticus?

There's plenty of precedent in the Calixis fluff for Inquisitors trading Acolyte cells, and the fact that they're conscripted rather than hand picked, only makes this more likely.

...

I know you're an experienced GM, but I have some harsh, but I hope fair, criticisms of your ideas.

The scripting is much too heavy-handed for my tastes. You're literally forcing your PCs down the path of damnation, giving them no choice at all. And you're not accounting for the possibility that they'll do the honourable thing and blow themselves to itty little bits to put an end to it. Usually taking away control of the PCs ethics is a fantastic way to make a game suck.

You're running at least one, and more likely two, massively super-powered GMPCs alongside the party. Unless the players are literally superheroes whose secret identities are the IGs conscripted by the Inquisitor, they're going to be overshadowed and out done at every step by your GMPCs. Which, as with the above, tends to be a really fantastic way to make the game suck.

Your plot twists, as presented, also reads like novella style plot twists where the meta pay-off is that the reader can't guess what's going on. RPGs, generally speaking, require the opposite to avoid going off the rails or at least becoming horribly confusing and boring. A handy rule of thumb is that there is no subtle in RPG.

Ah, sorry, I've not been quite clear enough! I'll address the issues as you raise them!

I'm just more keen on using the Ordo Hereticus, but like you say, I can just trade them or see how it works out.

I've presented it as a railroad campaign, but it's just part of what's going to be going on (illegal organ trade, drugs, anarcho-liberal uprising etc). I'll have other things for them to explore and things I'll wing and come up with on the fly, but I always create factions with goals, allies, motivation etc. to make improvising easier. Granted I won't be running it quite as sandboxy as I'd like as I'm not 100% confident in my rules management as I'm new to DH.

However, I don't see how I've damned them?

The two NPCs are not gonna be doing anything - the Inquisitor will be injured and out of action, while the Deatwatch is there to bodyguard him, so they'll be sending the party out to find things out.

It's not as much a plot as it is what I mentioned earlier - just what the Alpha Legion are up to.

it is fine to use the Alpha legion and the word bearers legion to advance the story but anything that would have killed a deathwatch team is way more powerful than little old humans could survive. The plot works but keep to a minimum what the Space marines NPCs do, the alpha legion does use regular humans as pawns in their overall chess match. Let the players choose to use the artifact or call in their boss and they can get rid of the artifact.

it is fine to use the Alpha legion and the word bearers legion to advance the story but anything that would have killed a deathwatch team is way more powerful than little old humans could survive. The plot works but keep to a minimum what the Space marines NPCs do, the alpha legion does use regular humans as pawns in their overall chess match. Let the players choose to use the artifact or call in their boss and they can get rid of the artifact.

I figured if the Deathwatch squad was essentially killed by the betraying Alpha Legionnaire, who armed the Cultists with anti-power armour ammo (they used it during the HH), traps, surprise, sheer numbers etc etc. I feel that would make it easier for players to stomach, while at the same time giving them a feeling of being horribly outnumbered and well in over their heads.

I usually have a few factions in each campaign I run, so I was gonna run Anarcho-Liberal secessionist rebels, Word Bearers and the Cult, Alpha Legion and the Hydra operatives, the State, Inquisition, and the PDF. Depending on what the PCs do this'll affect the outcome of the planet - Does it secede from the IoM? Does it fall to the Word Bearers? Or does the PDF seize power to stave off anarchy?

should work, just be careful