I was just watching a few episodes from season 1 and had forgotten how significant the entire concept of "The Pattern" had been to the early episodes. Was it explicitly part of the Blue/Red Cold War or are we to believe that it was connected to what we saw of William Bell's actions in Season 4 (though that was technically an alternate timeline?
I think they just called it "The Pattern" because they hadn't yet figured out what was behind it. Once they knew it was caused by the factions in the inter-universal conflict battling each other, they didn't have to call it just "The Pattern" anymore.
The pattern was what they called all of the unexplained events. Later we discovered that everything was caused by or related to Walter's trip to the other side. It is a little glossed over since no one ever says "The pattern was caused by Walter!" But it's clearly there if you pay attention. I did a re-watch of seasons 1 and 2 to see how the show transitioned and it did a pretty good job of shifting from pattern stories to other side stories while keeping them connecting. I don't think the show initially planned to have Earth 2. I think they originally were going for more of a conspiracy angle, but they've done a great job of shifting focus over the years while still making older stories matter to the ongoing saga.