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I ran into something similar. If you read my post, Something Really Odd, back on page 7 or 8, you'll see the details. I had only destroyed 5 or 6 arrays and Harper told that intel was useless because I had destroyed all the listening posts. Problem was, I had that mission to find all of those minor arrays and suddenly, poof it's gone. I had completed the Last Watch and was going after all the remaining arrays. I have a feeling that if you take out the major arrays, it clears out the quest about finding all the minor arrays even though there's a list of 14 to 18 them to destroy. Whether or not those 5 or 6 arrays that I took out were the major ones, I don't remember. There have been several people, both on PC and XBox reporting this.
If you killed all five major array hubs (they are named e.g alpha, kappa, omega), then yes, that is the end of the array loop. This is not the end of the questline - the finale is seperate, and is triggered after progressing through the vanilla questline (it should trigger after In Their Footsteps is complete for non-unity saves).
I ran into that as well. The very last listening post and hub I took down was a major fight between spacers and Watchtower soldiers when I landed.
Once you've completed The Last Watch, how many of the named, major arrays should be left? I suspect that I actually took them out and didn't realize they were the major hubs because they show up under the "Activities" section with an entry such as " Locate Watchtower Array Hub Kappa" . When I looked in the "Missions" section, I had the mission "Watchtower Major Arrays". When I opened that, I would have anywhere between 14 to 18 star systems listed. That's confusing if the mission is to go after major arrays, then that's where the named hubs like Kappa, Alpha, Omega and such should have been listed, not down in a minor activity.
Is it checked off in your completed missions list? It's the last big mission. It involves the Heimdall Station. I believe there was a huge battle on the ground and then inside an orbiting hub.
