I'm sad to report that there's a distinct decline in the Matrix Online storyline with the departure of one of the key developers, Rarebit, who was the driving force behind the game's story and development. It was he who revamped the mission system and personally undertook the creation of new cinematics. It looked like a new era for the game, but apparently it was not to be and for personal reasons he has left the game and our last update boasted new items and quests but no continuation of the story.
It's too soon to say what will happen to the future of the Matrix, but for now I'll carry on passing on the history of the game to you and hope that more content is on the way.
Double Cross was an interesting event as most of it took place on the forums and it wasn't a global event like many of the previous ones, this was largely due to having to scale down the ambition and scope of the game, but it was still action packed and full of intrigue.
A Tangled Web
There was still a lot of chaos left over from the Kill Code event, a few remaining Red Eyed Agents were prowling looking for something only they knew of. Morpheus was gone, but someone looking a lot like him was continuing the code bombings and the mysterious masked men, now identifying themselves as "Cypherites" were coming into the open and recruiting operatives from each side. If this wasn't enough, the Assassin was still about, indiscriminately attacking redpills. Times were hard, and about to get harder, especially for the crew of a certain Novalis 2.
Along Came a Spider
It came as a shock to all: Vashuo, engineer of the Novalis II, was dead. Not killed in action, murdered by someone from within. This surprise murder shocked all organisations into action, all eager to solve this mystery and explore its implications. Transcripts were found as well as code fragments, apparently from a phone signal meant to kill the entire crew, and would have, but for the intervention of the Operator. These fragments were tracked down in the Matrix to reveal a horde of information.
This code was deciphered and details came out: Toorima, a crew member of the Novalis 2 is responsible for the murder, confirmations come in to Zion and the other organizations. A new rumour spreads: the mysterious "Veil", a high ranking Cypherite, is involved in the deed. Shortly afterwards Zion confirms their findings: Toorima is none other than Veil and is now in Zion custody.
Zion have no time to mourn Vashuo or celebrate their victory as Enmascarado, another high ranking Cypherite involved in previous atrocities, comes out into the open taunting everyone, especially the Assassin. Niobe investigates and the Assassin shows up, launching a huge brawl in the city. Niobe takes the offensive against the Assassin, but the killer is a powerful enemy. He gets the upper hand and as he does he puts a bullet into his taunter: Enmascarado, downing the Cypherite once and for all. However, the aggressor didn't plan on going down quietly and rigged his body with the deadly Flame Virus which perpetually burns and spreads like an infection - the fighters had to disperse to stop the spread of the code, leaving the Assassin to escape once again.
This was not an easy day for Zion, but they could at least rest knowing they had done their jobs and the two Cypherite killers were down, one dead and another in a cell. They had earned a reprieve - but there was still a job to finish.
(I refer you again to MXOStory, where I got a lot of the details and images from)