After some digging, it appears that the novel "Psychotrope" is all about Mirage's awakening and its very first Otakus. I'm reading it now and will probably highly recommend my players to read it too - especially the one playing Mirage's Otaku.
Apart from that, the campaign and adventures are starting to coalesce in my mind. Some ideas thus far...
Jormungand worm: the Jormungand eggs are prepared in advance at certain key place in the matrix. An egg has been discovered by GOD (or equivalent for 2064?). The infected hardware is brought to a specialized facility to asses the threat. The facility is completely cut-off from the matrix to avoid anything bad from escaping.
Pax enlists the runner (meeting with the Johnson in the matrix) to infiltrate the facility and insert a specific chip she has prepared in advance directly in the aforementioned hardware (chip will be delivered separately by one of Pax's Otakus once the runners accept the job). The payload of this chip, unbeknownst to the runners, is meant to do two things. First, it will release Jormungand, or at least an enfeebled version of it. Pax's intention is to completely wipe out all data compiled thus far on the egg from the facility to not leave any trace regarding its nature. Secondly, it will delete the virus itself - for the same reason (this should not be something simple to do, but one can imagine that the enfeebled version is purposely released with a limited lifetime instead).
The Otaku of the group will probably want to inspect the chip beforehand, but will only learn that it is meant to enable "something" and then delete any traces from this "something". Nothing big enough to back off from the run anyway.
When he activates the chip, I plan something seemly impossible to happen: Mirage will address the Otaku directly, even though he should be cut off from the matrix. I'll not give any justification for this as I don't mind an AI like Mirage to have its secrets that mere mortals cannot begin to understand. Anyway, Mirage will be direct and very clear: "Disconnect yourself, now!". I'll be very clear to the Otaku that Mirage is not joking - at all (I need to read more on this, but at least in previous editions a Technomancer was able to do that).
At that point, Jormungand "Junior" is released in the facility and all hell breaks loose. Lights go out, emergency power supplies are activated. Maybe the runners' commlinks will sizzle and fry, bricked by the worm. All corporate deckers that were currently investigating the egg in VR die. The Otaku, thanks to Mirage's forewarning, escapes this gruesome fate. Even if he's usually very comfortable in the Matrix, he will suddenly find himself in what seems to be a very alien and threatening territory, with the impression that something is lurking and waiting for him in the shadows. Jormungand Junior is no more there, but the facility's host is nevertheless heavily corrupted by the Dissonance. Even the other runners will understand that something bad is going on just by seeing his terrified face.
The run ends with the escape from the facility. Corporate forces will want to contain everything and everyone until they can make sense of what happened, so this should be the point where a direct confrontation is probably unavoidable, even if the face and hacker did a good job of infiltrating the facility discretely up to then.
The network: someone - maybe Overwatch - will want the runners to exfiltrate a node loyal to Megaera. At that point, the Johnson doesn't know about the network yet, but has suspicions about the Megaera node (to clarify). Deus is aware of that node's condition and keeps a close eye on it, without having decided to eliminate it yet. All the target's colleagues are in fact Deus nodes. When the runners attempt the exfiltration, seemingly harmless corpo salves will suddenly be taken over by Deus and become a highly dangerous and well coordinated opposition (thanks to the skillwires every node has) that will try to prevent the Megaera node from escaping Deus' grasp. I picture the scene in my head: harmless scientists suddenly all staring at the runners and threatening them: "Insignificant insects, how do you dare oppose me", or something along those lines. With one node starting a phrase and another one finishing it. All the while moving to surround the runners like predators about to dive in on their prey. Anything that will make the players freak out.
Should end with an escape where Deus wreaks havoc in the matrix and tries to stop the runners by any means. Hacking gridnav to send their vehicle at the wrong place, etc. In the end, Deus, will kill the Megaera node with lethal biofeedback. The node's last words should give the runners a hint as to its nature (they should remember Megaera's "naive" and/or damaged condition and very distinctive way of expressing herself).
Winternight: Not sure how yet, but I plan for the runners to discover one of the nuclear warheads they have prepared. I believe the players are mature enough to not try to set the bomb off "for the fun" and see how the GM struggles after that.
