Referred to some as Chapter 1.4, Choice and Consequence was more of a min-event than an in-game chapter, but is notable for introducing us to a new Zion crew, some of whom would come to play a key role in the Matrix. It is also notable for letting players choose the fate of one of the crew at the end of the chapter, which was interesting, but a little awkward from a storyline perspective, but anyway - we'll come to that later.
Zion formally introduced it's operatives to the crew of the Novalis 2. Novalis had been a hovercraft operational before the truce, but that went down during Smith (as Bane's) sabotage. The crew were killed, but the hull and systems were salvageable and so an up and coming crew were given the craft as their own. This was the first of the recommisioned fleet, as the Military started to move it's assigned redpills out of Hoverbarges and into independant ships. Read more about the crew in this detailed report.
Meanwhile, all organizations were still reacting to the loss of Morpheus, though each in their own way and with their own perspective. Also the mysterious masked men were upping their presence in the Matrix, openly attacking redpills and others. Two leaders emerged, one named Enmascarado, another Gemaskeerd wearind distinctive coloured bandanas as opposed to the gray most of their group wore. Reports also came in of attacks taking place in the real, which were linked to the group, making them very dangerous indeed.
Things weren't going too well for Zion's premier crew either, one of their number - Neurophyte went missing and this was linked to a very dangerous and very desirable "killcode" making her a target for all organizations. A killcode is naturally very dangerous and a type of killcode is rumoured to be how the Assasin knocked off Morpheus.
[From here events vary depending on what server people played on, but I'm going with the most popular choice and the one that makes the most sense with following stoyline]
Neurophyte was eventually tracked down and rescued by Zion, but things weren't as smooth as might be hoped. The killcode was actually implanted in her mind and killing her slowly. Neurophyte insisted that the code be saved to keep it safe and as a potential weapon for Zion forces, but as this would cost her life Zion operatives rallied to support her and the decision was made to save Neurophyte and lose the killcode...which may have been for the best after all.
While this was going on operatives tracked down the bases of the Masked Men and defeated them, but it was certainly not the last time they would play their part in the Matrix. The same could be said of Neuophyte and her crew, who were now on a well deserved leave. Neurophyte had more to do and there were some on the crew yet to fully reveal their role in the ongoing story.
Right, that's it for this for now, I'll get you caught up with Neurophyte's next adventure after giving you a bit more info on what you can do on arrival in the game, that and some other stuff