Season 2 Star Trek: Picard scenes were written to clear up the confusion with Dr. Jurati and the Borg

Star Trek: Picard season two confused some fans when Dr. Agnes Jurati united with the Borg Queen. Many were wondering if that meant the Borg had "gone good" and if they would now be an ally in the Federation's future. The confusion intensified when Picard's season three once again included the Borg, but they were still the enemy. So what had happened to Dr. Jurati and what was the point of her uniting with the Borg Queen if the Borg were still going to be against the Federation? As it turns out, according to executive producer, Terry Matalas [via Trekmovie], there were scenes written for season two that would have clarified things.

Matalas acknowledges that there was some misconception that the Borg had changed after the season two finale, and they would be good from that point forward. However, that would have negated Wolf 359 and would have also had a negative effect on Picard season three. So an explanation had been written where Dr. Jurati says she stayed out of history's way and that, basically, the Borg she was with was just a small collective and not the entirety of the Borg.

"“Jurati’s Borg, there is a misconception that they are the Borg in general, that the Borg were good [after season 2], which would have undone Wolf 359, which would have undone Picard, and none of the future they came back to would have looked the same. I was off working on season 3 as those final [season 2] episodes were written. And so we were reading scenes that didn’t end up getting shot. There was a brief scene with Jurati in which she explained that she stayed out of history’s way and they were a small collective of Borg, but they’re not the Borg of tens of billions of drones or anything like that.”"

- Terry Matalas

The Jurati Borg storyline was supposed to wrap in season two just like it did as it was never meant to be a continuing story. The writers did have more dialgoue incorporated into season three to offer an explanation as to the transwarp conduit at Jupiter that Jurati was guarding. It was simply meant to be a distraction so Picard's Borg Queen could fulfill her evil plan. According to Matalas, there was a "whole thing" about it.

"“So while Jurati Borg was always going to be the payoff to [season 2], it was never really intended to be a longer-running thing. At the last minute, we added the thing where there was the hole that was going to open up and destroy—they added that to give a burst of action to the [season 2] finale, to give her a reason to do all of this. So that started to become retrofit into, “Hey could this be something for season 3?” But we were already way down the line on what we were doing with it. So you could say that she was guarding this thing. We did have a line on the Enterprise-D from Riker—when he talks about the Borg transwarp conduit at Jupiter and that the one that Jurati was guarding was a distraction, the Queen’s way of saying, “Go over here.”… We had a whole thing about it. But when we got to the cut, it was just like this big exposition dump that was like, nobody cares. His son is on board, Starfleet is assimilated. There’s this giant thing and now we are retrofitting and explaining the Jurati Borg.”"

- Terry Matalas

There was so much going on in season three of Picard that adding additional information about Dr. Jurati's integration with one of the Borg Queens would have just been a minor payoff. Fans had already seen several Borg Queens, thanks to Star Trek: Voyager and Star Trek: First Contact so I think we all understood that Dr. Jurati's union with that particular queen on season two hadn't eliminated the threat of the Borg. It didn't take us long to realize that once we got into the final season of Picard.