Disclaimer: I am posting this for 3 reasons. 1. I'm bored. 2. I've been drinking. 3. I'm lazy and figured putting my existing ideas out there may get some ideas in return.

This is how I'm running my, I don't care about power-creep balls to the wall, open world Ascension game:

The group (Inquisitor, Vindicare Assassin, Templar Calix Interrogater, Magos, and Stormtrooper) ran through the Ascension book pre-made, Red Wake, with little trouble. By little trouble I mean the Inquisitor had to shoot the now Magos' previous character (Desperado) for heresy. It happens. After that I told them it's entirely up to them where to go and what to do.

So, this is what I do. I came up with roughly 10 one to three session story arcs and have seeded them throughout the campaign (which means whenever I remember them). A NPC will bring up something that is happening on another planet, the Inquisitor's lone Acolyte group will dig up something he will deem is appropriate for him to handle, or some other Inquisitor/Adepta member/old friend/etc will go to him for help. It is up to the group to decide what to investigate, what to dump off to the Acolytes to handle, or what to ignore. These story arcs may or may not have timers and may or may not have significant impact on the Calixis sector itself. (I should probably say that my group consists of players that have been playing RPGS together forever and work together well). The power-creep problem I have, sort of, solved by the players own horrible "insight" and the judicious use of horde rules. They can carry around all the armor and weapons they can requisition but when they go on to certain planets or go undercover they only have what they can bring. Sometimes they plan accordingly.... and sometimes they burn fate points.

Here's where the lazy part comes in... I'll lay out my story arc ideas in the next post for people to steal and say they came up with them because they are incredible and then you can give me yours which I will steal and say they were mine because they are hopefully incredible. We all come away with bigger egos and lots of win.

TL:DR - srsly read it. You already clicked on the post.

Right well, let's have it then

Story Arcs -

Completed by group:

Warp Whispers (Malleus themed):

Astropathic choir "Hymn of the Ever Burning Star" members are dying. Investigation leads to unassuming Orbital Object 366-A-7x above Scintilla where the astropaths are under a quarantine by the Inquisition. Astropath members' heads are exploding, eyes liquefying, and other pleasantries when sending/receiving messages and opening themselves to the Warp. Sitting in on a session with the astropaths is the obvious and eventual answer where it leads to a showdown with a demon of your choice. I used a homebrew warp assassin themed off of the Slender Man with a horrible psychic backlash. It almost killed the Interrogator. Almost = not good enough.

Soylent Green is People (Hereticus themed):

House Maken splinter group on Malfi begins to look for partners in new agri-business. They have acquired a recipe for a very cheap new high protein algae flake food source. Investigation leads to secret ingredient being human flesh and demonology. Getting the recipe leads to one crazy Magos on servitor manufactorum ship. Stealth would be a good idea to getting the recipe from House Maken but when it comes to some players.... walking through the front door and demanding it "works" too. This one is still in progress.

Warpshade (Xenos themed):

Budding Hive planet Draaken is enveloped by a supposed warp storm and an Inquisitor sent there has disappeared. Investigation leads to the planetary governor being overthrown by a political group known as the Colored Mirror who all dress in dark robes and have bald heads. The Colored Mirror is either infiltrated, or in my players' case, invited to dinner where they are attempted to be assassinated and then nearly overrun by the genestealer cult horde. For some reason the Magos thinks he can 1 v 1 the Purestrain genestealer daddy but eventualy the players win the day. You can either end here or do what I did and turn this into a long one by having them walk outside to mycetic spores raining down upon the hive. With a Mechanicus Sect's help they realize a tyranid hive ship is buried deep in the planet and the tyranid swarm descending on the planet is actually queen-less and striving to reach that ship. Now it's a race to get to a buried hive ship and blow it up. Or you can just stop at the genestealers.

<edit - Planet and Hive Draaken is extremely detailed by myself with Imperial guard detachment, PDF forces, and culture/planetary info. All is available if anyone cares.>

Story Arcs-

Completed by time/events/others:

Chains of Duty (Malleus themed):

Rumors of penal legion ships disappearing in the warp. Investigation reveals a Techsorcist Paxius investigating a pattern involving the disappearances. Sheol XVII is next penal colony to raise a legion and Paxius suggests going undercover as prisoners on the March of Terra galaxy-class transport. On ship a Pilgrims of Hayte Prophet of Truth emerges who convinces the prisoners to revolt. The Prophet of Truth is actually forming a fleet of corrupted penal legion ships to throw at planet Synford, which is a Baneblade producing forge world. This story arc was completed by rival Inquisitors as it was passed on by my players. In hindsight this is good as going undercover as prisoners would only have ended really badly. Like really.

Open story arcs:

Space Rocks (Xenos themed):
Rumors of an asteroid mining expedition being torn apart leads to the war planet Kulth where Orks have begun using very un-Orky tech to hurl asteroids at the planet. Void suit melee battles against Orks floating in space is a must. Because why not.

Ghostfire Alternative (Hereticus themed):

New unapproved combat drug begins to appear among guardsmen, mercs, and such. Obvious Iocanthos possible tie-in as surely someone is upset over a drop in Ghostfire sales. The new drug Ethyria puts you into a pleasure filled stupor in your mind while your physical body goes berserk. Eventually discovered the drug causes mutations and is being financed by your local Mutant terrorist organization. Yay!

Shadow Strike (Hereticus themed):

Officio Assassinorum rep asks help in smuggling a renegade planetary governor's nephew back onto the planet after being indoctrinated as an assassin. Who would tell the Officio Assassinorum no? Very easily make it onto the planet and into his personal mansion where you fall into the trap and the assassin is now killed and somehow (maybe) the players escape. Now you're alone on a planet where everyone wants to kill you. Possible help could be in remnants of loyalist PDF/Guard/Arbites and throw in the twist that the Planetary Governor is actually a good guy and is revolting for whatever pansy humanitarian reason you like. Moral quandaries are the best quandaries IMHO.

Krimson Tide (Hereticus/Xenos themed):

Brandt Strophes (nephew to Laurent Strophes from Purge the Unclean), an ex-Arbitrator, brings attention to gangers on Scintilla using xenos weaponry. Nobody cares yet since it's gangers killing gangers. Investigation leads to bloody battles (or you can use stealth if you're into that kind of thing) with gangers using Dark Eldar splinter weaponry and the capture of Jorra Forsythe, a smuggler. He leads you to a Krimson Cabal ambush on 41 Pry. Who doesn't love a good Dark Eldar ambush?!

Mad Cow (Hereticus themed):

Lizard... cow.. whatever. Someone is splicing tyranid DNA into grox herds to make them bigger for more meat. Other extreme side effects occur and for some reason people get mad when dinner tries to eat them instead. So bring on the Inquisition to head to Cyrus Vulpa and find out what's going on. Probable velociraptor-esque mutations would be interesting as well as the show down with whatever bad guy as I've already used the crazy Magos idea.

Very nice.

Return ideas:

The Inquisitor has been asked to investigate an upsurge in piracy in the Drusine Marches - specifically targeting trade to and from port wander. Most ships travel under navy protection in convoy but these are being hit after the convoy reaches 88 Tanstar and disperses. They're getting shoreside intel from someone, and it's very good intel. Also, several raiders acting as a squadron rather than lone individuals - and they're well-handled to the point that the navy's already lost a frigate caught on solo patrol by them.

How have the pirates put a force together - particularly the trained crew, as well as the light warships - and where is the information coming from.

Post the Red Wake (which they're doing now), the players have, again, a free choice of how to proceed in the investigation, along with several side-distractions to keep them interested.

Initial missions:

1. Hunting down the rest of the menagerie on Malfi - the Thrungg raid from Black Sepulchre is a nice therapeutic violence session.
2. Tracking down the raider ships. The only decent auspex data on the attacking ships to date came from a House M'Kao ship called the Tatsu which was attacked in the Threnos Zone. Lady Sun Lee has provided auspex data on the attackers to the Navy but the recording is lower quality than it should be (making it next to useless for identifying individual raider ships against Ordo and Navy records) and carefully 'edited' for content/timeline. The players need to find some leverage to 'persuade' one of the most influential rogue trader houses in the sector to play ball with the investigation. Figuring out what the hell they were doing in threnos when they were attacked and what (or who) they're trying to hide might be a good start.
3. Tracking down the crew. Whilst any 'scruff from the docks' can be dragooned to haul a chain or heft a crate, a squadron of raiders still needs hundreds - maybe thousands - of semi-skilled and skilled crewmen to fight the ship effectively. If they haven't earned their experience on the raiders, then they must have been trained aboard a warship somewhere - either demobilized or discharged navy crew, system defence fleet veterans, or crew from especially well armed rogue traders.
4. Investigating the victims. Several ships hit by the raiders are simply 'missing', but the hulks of others - gutted of crew, cargo, and any other viable salvage, have been found. Investigate and gather whatever clues you can. Of course, digging around in a half-derelict ship is entirely safe. Also, look and see if you can find any clues shore-side; if someone's providing information on the victims, there may be a clue on who based on any connection between them.
5. Track the loot. Ultimately piracy happens for profit. Disposing of valuable salvage - especially the kind of exotics that turn up on koronus-calixis trade route ships - in bulk is difficult. However, the hive world of Piety is infamous as a hotbead of scum and villainy, and if you can dump that stuff anywhere in the subsector, it's there. If you can find out some of the more...err...unique (i.e. ilegal) items the ships were carrying, maybe you can find them and track them back from buyer to middleman to seller. Of course, people engaged in the cold trade are sometimes hesitant to provide accurate ship's manifests to the Ordos, so some...err...creative persuasion...may be needed to acquire them.

looks like a fun thread here. I"ll jump in with some.

The Forgotten Saint: (Hereticus/Malleus Themed)

On Orendal's Tomb, heretics are working to pillage the graveyard shrine-world, hoping to find the resting place of Orendal. Orendal is a saint of the Ministorum, but the truth of his life is a lie: A select few have learned that Orendal was in fact a titan that was felled during the crusades, and 'he' and his princeps crew were buried on the dusky world. Now forces move to perform black rites to 'ressurect' the titan, but first they must enslave the spirits of the fallen crew. The Acolytes must stop the heretics in a race against time, tracking down the grave-robbers and putting an end to this double heresy that threatens to pit the Mechanicus and Ministorum against each other if the truth is revealed.

The Xenophage (Xenos)

The Ordo Xenos operating in the Calixis sector have been developing a particular potent strain of pathogen targetted at wiping out a multitude of xenos species, primarily aimed at being used against the Orks and Eldar that plague the Segmentum. This xenophage, while still early in development, has proven to be remarkably effective in small scale deployments. Unfortunately, a sudden and rapid attack by Eldar Corsairs has seen the xenophage stolen. Imperial Strategos fear what the xenos might do with it - and worse among their predictions is a retro-tailoring towards humanity! Throne Agents, with assistance with the Deathwatch, must quickly mobilize to intercept the theives before it's too late!

Fantastic ideas!!!! I'm definitely going to use them. My players just survived, unfortunately, the Dark Eldar ambush on 41 Pry and will be going who knows where. Now I have some more worms to dangle in front of them!

...This is of course assuming any of the players survive the 'Red Wake'.

At the end of the last session, the group's somewhat eccentric Magos (who is after all a senior priest of the Ecclesiarchy's rival - and older - church) has just spotted a redemptionist priest at the ordination ceremony, and she's decided she wants to go "poke him a bit" about the "obvious logical inconsistencies in his religious dogma".

Not that this could end badly in any way.

The (Un)Willing Heretics: (Ordo Hereticus)

Your former Inquisitor stops by with mission he's been brewing for several years. A heretical cult dedicated to [insert random daemon/chaos god here] has been active for decades, if not centuries, in the sector and the inquistion has been unable to root them out. This cult is responsible for the inquistion declaring Exterminatus on at least one confirmed planet, and it seems one particuliar random hive world is headed in that direction also. So the Inquisitor, who is a truly devious and ruthless bastard decides that more "drastic" measures are required and gathers his most powerful and trusted throne agents around him (real catch prizes for the cult to corrupt) and has his pet psyker brainwash them into thinking they've become disillusioned with the Inquisition and Imperium and joins the forces of chaos and the cult in question.

This was several years ago and the Inquisitor thinks it's finally time to hunt them down and learn all the juicy details they've accumulated in their forced heretical life. Enter the players whose job it is to perform that task.