No, sorry. My personal experience and the devs themselves says otherwise.
- Uncheck integrate: you get the story mission on the Geoscape, and the Rulers don't appear until you do the mission (this is what I did, and what is happening in my game)
- Check integrate: the story mission is disabled, and the Rulers are moved to ADVENT facilities (I've seen this in a Let's Play)
Something must be up with your game because they aren't suppose to appear randomly no matter what option you choose.
This is from the AMA Firaxis recently did:
Q: From what I understand integrating the previous two DLCs with the expansion removes the two story missions. What was the rationale behind that? They are such a blast to play through.
A: War of the Chosen doesn't remove the missions, but it does disable them if you use our "Integrated DLC" option to balance the DLC content (particularly how the Alien Rulers work) with the new expansion features. You can still play both of the DLC story missions if you turn off that integration! Both the Alien Nest and the Lost Towers mission happen very early in the campaign, and we wanted to add another big narrative mission for WotC (Lost and Abandoned). Having three huge, lengthy missions back-to-back would be really draining for new players, so that was one of the reasons we turned them off for the default experience.
Q: As a follow up, if you opt to turn off the Integrated DLC option does that not keep the balances made to the enemy units/sparks?
A: No, the balance changes will always be there.
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