So what I got from what we were presented, & help me if I'm wrong...
There are rumors that Gideon escaped during a transfer, but it's trying to be kept quiet or outright dismissed.
There's enough information retained about the work Pershing was doing, but they didn't know the exact process, so by having him select the EXACT equipment he needed, they're confident they can figure it out.
Based on the 'Previously On', the communications officer was planted by Gideon into the system, expressly to get to Pershing after his capture & turning over to the New Republic.
So, unless I'm missing something, Gideon will be revealed to be the season's big bad, only now working directly with the early, organized First Order, instead of random Imperial remnants.