I put this up here for the use and utility of anyone who cares to read and comment. I don't consider it by any means "difinitive" but I hope any ***-bits of knowledge I can help spread will someday be of use to others.
Dark Angels - The Fallen.
-A tantalising hint concerning the "Great Secret" is within the grasp of the battle brother, if only he would go off mission just this once... (Part of a "Fall from grace" type plot. Does the Dark Angel choose his team over his chapter, who are his real brothers. Recomended for established Kill Teams)
-Some prisoner or scrap of inteligence gives rise to a possible clue to the location of one of the fallen. (Classic Dark Angels)
-A chance encounter with a Ravenwing Recon group stalking the same target as the kill team leads to a tense stand off, the Ravenwing will not expose their chapter's secrets to outsiders, even if they count one of their own amongst their number. (Lets hope the kill team don't want to take on the Ravenwing, that said, the last time this occured in a narrative tabletop game... well... it got interesting to say the least.)
Note: By far the most prevelent theme of any Dark Angels plot thread is "divided loyalties" rather poeticaly echoing the original rift between luthor and the Lion. Nice moral dilemmas for a Dark Angels PC, especialy if they've been "bloodied" with their kill team. Seeing the actions of their chapter's darker side without perhaps being fully initated into them in a controled manner can cause some hard moral choices to be forced upon a Dark Angels PC.
Blood Angels - Curse of Sanguinius
-A chance disocovery in a laboratory complex the kill team has been sent to "cleanse" may contain new information on "The Flaw". Perhaps the actions of a rogue magos biologis could save the Blood Angels from their perpetual curse and restore the chapter to a second golden age. (Very generic example of the many possible plots that could look similar to this.)
The Black Rage, rapidly sucumbing to the tumult and insanity of his chapter's curse, the battle brother steels himself for what must surely be his final days, visions of his beloved Primarch begin to haunt his dreams and even creep unbidden into his waking eyes. (Handle with care)
Imperial Fists - Wayward Sons
-Inteligence reports place a contingent of the heretic Soul Drinkers chapter within striking distance. The vile xenos lovers and sorcerous heretics must be expunged at all costs, but a prisoner would give valuable insight into their abberant behaviour. If he could be made to talk... (Want to do something with Necrons? Good place to start. Also very good generic plot hook depending on how familiar you are with the chapter.)
Space Wolves - Mark of The Wulfen
-Cursed with mutation or blessed with the gift of Russ, a kill team of deathwatch are dispatched to a lifeless troop transport, to find it's blood soaked hallways and deathly silence the work of a pack of bloodclaws who succumed to the Canis Helix in full and became little better than mindless super-predators. (Survial horror game, good fun.)
Red Scorpions - Return to Beta Anphelion
-Inquisitor Solomon Lok isn't quite dead. A single barely audible distress call eminates from the dead world. Hinting at a treasure trove of vital inteligence about Tyranid xeno-forms, their biochemistry and their methods of waging war. (Beta Anphelion is of course a dead world now, ash waste pock marked with tunnels and ruined explorator bases. Think Jurassic Park meets the mummy. Are the Tyranids realy gone? Is the distress call genuine?)
40k Historical - The Taros Campaign
-The World of Taros, currently in the hands of the Tau is to be retaken by a combigned force of Titans, Astartes and the might of the imperial guard. But mindful of his green troops and the nature of the terrain, the Deathwatch are asked to provide their specialist expertise to ensure the Campaign's sucess.
-Imperial Armour Volume 3
-In essence this campaign can work as a streight up sand-box military campaign or as a structured narrative refight with the deathwatch called into assist once it appears the campaign has stalled. The Deathwatch can then perform some surgical strikes knocking out keystone assets of O'Rymr's forces such as the RX-10 Tiger Shark bombers and Manta transports from the ground in night raids reminiscient of the SAS during the north african campaign of WW2. (The actual inspiration for IA Vol3 was the WW2 N african campaign in case you missed it )