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I am curious about opinions on two hypotheticals:

1. A company of Space Marines enter a system infested with Orks, before they can finish cleansing the system a Warp Storm springs up and cuts them off from the rest of the Imperium. After they eliminate the Orks what is their next step? Do they risk the Warp Storm? Attempt to traverse the storm while in regular space? Wait for the storm to pass? I can imagine any of the above depending on the chapter.

2. Instead of a company it is a successor Chapter and one of the planets in the system is designated as the location of their new Chapter Fortress Monastery. Do they settle in the system that may be cut off for centuries or attempt to slip through the Warp Storm? I imagine most new chapters would settle in the system.

Well it also depends what is coming out of the warp storms, they could have Chaos Marauders/Marines or demons so the chapter may have to settle because after cleansing the orks they might have to start cleansing the taint of Chaos.

Depends if its a regular warp storm, which only affects the immaterium, a hole-in-reality warp storm like the Malestrom and the Eye of Terror, or if its a Bow-wave Storm kicked up by a massive fleet travelling through the Warp.

I was thinking that it was the less deadly cut off from the astronomicon and dangerous to pass through type, and less the rift in reality type.

If it's simply a matter of not being able to travel via the Warp, the Space Marines simply dig in and build fortifications, comm-shrines or whatever else they have the materials and resources for.

Especially if this was a cleansing of Orks, they can be reasonably sure that there will be another outbreak later on, as whatever spore-pods were hidden away give rise to more Orks in the future.