so I have thought a bit about this topic. I am planing now for two missions, since I am GMing once for my friends and second on a RPG convention. The main mission is supposed the the convention and has the major topic about Achilus.
The first mission is supposed to be a Prequel. I have the following idea:
The Deathwatch learned of a High Ranking officer who is a loyal member of the Children of Achilus. This officer is part of a military force which fights an uprising on [insert name of the planet here]. The Kill-Team's mission is to capture this officer to learn more about the Children of Achilus and maybe something about his disappearance.
When arriving at the planet, the Kill-Team encounters heavy military involvement. Multiple cities (Hives?) have joined the rebels and the planetary defence forces, together with called military reinforcements, are pretty busy in fighting the rebels.
Now I try to build the first decision for the players: The Kill-Team is asked to help at some heavy warzones. Maybe the Kill-Team is not interested, since they have their own agenda. But on the other hand, the Deathwatch has to protect the Jericho Reach and the Space Marines as members of the Adeptus Astartes are to protect humanity itself.
Maybe the Kill-Team ignores the pleas and ask for the location of the high ranking officer. They learn that he fights a rebel base hidden between some mountains. When they go there, they will quickly learn that the base is build upon some ruins and the high ranking officer uses the whole war as a mere distraction for his own exploration. He knows, that some secrets are hidden beneath the ruins.
Now the question: What could there be hidden which relates to the disappearance or Achilus itself?
Furthermore I want the plays to face some consequences, that they did not answered the pleas. What could happen if they finished there job in capturing the officer? Maybe the rebels got some reinforcements or ? Maybe they face some true challenges in leaving the planet?
On the other hand the Kill Team could answer the call and help the PDF in the first place. Now the Kill-Team should learn, that a Tyranid infestion has taken place and the uprising is due to the second or third generation of Genestealer infestion some years ago. Whatever they do, at some point they will notice that they have to go on with their own mission.
Now what could be the consequences of giving the high ranking officer more time in beneath the ruins? Did he dig deeper and made it all the harder to capture him? Is he even finished and the Kill Team has to follow him to the stars and even inside his space Ship? Thus they would never learn about the secrets beneath the ruins, because the simply noticed that 'he-is-back-aboard-his-ship' ?
What could increase the tension? The presence of another space marine chapter? Putting some pressure on the Kill-Team to help to defend the planet? A traitor? Another, not so high ranking officer, who passes vital information to the high ranking officer in search?