I did not witness these events first hand. I was unplugged for some much needed R&R with some real-life T&A. The Lady in Red has her wiles, but there ain't nothin' like the real thing baby, and no amount of jacking in can replace that. Never fear, my sources have filled me in.
Zion sent out a relay, introducing us to the crew of the Novalis II. Captained by Sawaka, this is the first hovercraft since the war, and the Zionites are happy about their accomplishment. Most people jack in through hoverbarges these days, which is convenient, but also leaves us vunerable to attack should the truce break down.
Reports on Morpheus and the Assassin circulated. These are accurate enough, but they also seem to contain encoded messages. It always pays to look beyond the surface.
The Masked Men were at it again, attacking redpills throughout the city, led by Enmascarado and Gemaaskeerd. They were operating out of three hidden bases, and Flood sent out order to locate them.
In other news, Zion lost one of their own -- Neurophyte from the Novalis II. Apparently, she got herself in trouble when she found a "killcode", and everyone was scrambling to get a hold of it. Flood sent out some clues, if you can call them that. Geography was never my strong suit, so I defer to those with more knowledge on the subject.
The hidden bases were eventually found and taken down, and the Masked Men were none too happy about it. They randomly attacked operatives of all three orgs. They have also taken their attacks outside of the Matrix and into the real, killing hundreds. If they wanted to make enemies of the other orgs, they have certainly done so.
Neurophyte was still missing, but new clues had operatives scrambling to find her location. These details eventually led operatives to the top of the Kalt Chemicals building in Kedemoth. It was there that Neurophyte was found and saved by Zion. Zion's collective sigh of relief was premature, for they had a tough decision to make. They had to choose between Neurophyte and the killcode implanted in her RSI. As expected, Zion chose to save Neurophyte and abandon the killcode. Doctors were unable to fully remove the killcode. The future effects these remnants will have is unknown.