I've asked this question in other forums, but I we won't be able to continue our campaing for a while and that's given me a lot of time to think about what I'm going to do next.
I am going to put my players in a very difficult situation. I'm going to transcribe my notes here if your curious as to how this situation came about. If your not curious, skip to the end.
1.)Players arrive at Watch Fortress Erioch, before they are even fully initiated they are pulled out and thrown into a ship. They are told that a inquisitor has called in a favor and has a desperate mission that needs to be undertaken IMMEDIATELY and they are the only Astartes available. When they are equipped I let them take weapons up to the distinguished level because they're never going to spend requisition again in this campaign.
2.) Players are transported to to a world called the Mire (I took this section of the campaign from two Black Crusade spaltbooks). There mission is to (Supposedly) retrieve a Chaos artifact known as the Axe of Khorne. Unfortunately, this world is overrun by chaos and is a major Death Guard recruiting world.
3.) There ship is shot down and they are stranded on the planet. Over the course of several sessions they learn that there are Khornate berserkers active on the planet and they are working with the Death Guard to retrieve the axe. They liberate a massive mobile sand-crawler that acts as the planets main city from Nurgle. They make contact with a imperial resistance movement on the planet that is being patronized by a mysterious inquisitor. And finally they repel an assault on the crawler lead by the Death Guard Company master. Finally, a contingent of Night Lords is hired to kill them and is repelled. They actually convince one of them to betray his fellows and work for them. All this happens as they are traveling across the world to get to the axe.
That's the campaign so far, here's what comes next.
4.) They have no chance of liberating the excavation site in a head to head battle. Over the course of the campaign they've killed 21 chaos space marines, they're are sixty left on world. So the traitor Night Lord (named Romulus), makes a plan. His war-band doesn't know that he's turned traitor. If he sends up a distress call they might come get him, in their stolen thunder-hawk. The players can then use the thunder-hawk to spearhead the assault the excavation site.
-This is what as a dm I call a "fixed point in time." They're is no way the players can be victorious without this thunder-hawk, they're are simply to many Chaos marines left.-
5.) After a massive battle, that should last a session or three. The players fight the Khornate chapter master, the Night Lord chapter master, the remaining Death Guard, and a horde of Plauge ridden zombie slaves that they've been using as workers the PCs should liberate the site. At this point they realize they've been given faulty info. The Axe of Khorne is not an axe, it is the name of a massive pre-heresy Lunar class light Cruiser that the chaos marines have been trying to recover from the planets surface.
6.) Here's what happens next. The Deathwatch track the PCs down and demand to know why they've deserted from their posts and stolen so much valuable equipment. No matter what the players do (FIXED POINT IN TIME) they are called heretics and have to flee from back into the ship.
7.) The Axe of Khorne is a total wreck, and has been rotting beneath the earth for 10,000 years, but it is still whole. The chaos marines have welded the Night Lords raiding ship to it so they can pull it into orbit where they can complete their work repairing it. A navigator they have with them (They saved him from their previous ship.) Can pilot the Night Lords ship and tow the Axe of Khorne with them into space and eventually the warp. They also discover that the Night Lords have been collecting pure gene-seed from the fallen traitor legends. Meanwhile the players are going to go into the Axe to turn on several parts of the ship so they can actually survive re-entry. There they find that 1. the ship crashed because it was overrun by orcs. 2. The is a population of human survivors who have been trapped on the ship since they crashed. They are descended from the ships slaves and now have a whole culture developed around killing and eating orcs. This section will also take a while to resolve. Eventually, they re-enter real-space near the navigators home world. His clan then puts them under their protection, after all, its not everyday a light Cruiser falls into your lap. They are then contacted by the inquisitor who put them in this situation.
T.L.D.R
Players are falsely accused of being deserter and traitors by the deathwatch. What really happened is that a Radical Inquisitor has manipulated them into their situation, which is currently ostracized from the imperium and in possession of a massive battle ship and thousands of Gene seeds. He did this, because he's become tired of going through official channels to rally military power, so he wants to own a space marine chapter, loyal to him, to carry out his designs. He gives the players a choice, work with him and create a new chapter under false identities. Or become exiles and fight to clear their names.
What do you think? If you were one of my players how would your react?