Possible Story Ideas

[Neoteny]

Finally found the notes I'd written on the direction I thought the story should've gone in following shut down. I have it written as a semi-in character/mission/event thing I guess (don't know why I did that) but here's the skinny:

Starts when Wright is killed.
Mauser appears, enraged, and confronts Zion about killing her.
Mauser reveals that he brought Lock to Wright's facility for treatment, then they left him there, destroyed most of what was around, and left in a small hovercraft and put out a weak signal to Zion.
Mauser acted as her operator and pilot while she experimented on herself, and used a simulacrum to explore and delete Wright's files.
Wright, using scans from Halborn and Carlyne was researching their abilities and eventually made herself into an Oligarch, but found it trapped her in the Matrix and destroyed as much of her research as she could so that no one else would find it and make her mistake.
Mauser reveals that Wright was attempting to help Zion beat the Machines in the war, and is enraged that they killed her. He claims that he is going to further her research and make a decision as to what he wants to do, but claims no affiliation to any party and halts communication. He'd be seen every once in a while, though.
He eventually decides to bury Danielle near the old Mainframe in Old Zion, where EPN is holed up.

The whole Trinity thing is a distraction made by Helian/Tesarova to keep everyone away from the real BIP, which is revealed to be Sati.
The Morpheus simulacrum approaches Sati and has her use her power to insert him into a pod body and become real. He explores the Real to make his own decisions about the world.
Helian and Tesarova steal Sati and use her to inhabit pod bodies following this.
One of them retains her on a floppy.
There is a hovercraft battle to recover her (decides who gets control of Sati and the BIP)

The wreckage of the Nabonidus is found.
The real Morpheus is found to have been in a construct all along (as a message to Merovingian players suggested was what the Assassin's bullets did), without any way out. With help from Zion and EPN, he is freed and restored to health over time.
Morpheus decides to go his own way and founds his own group of Morphites. Zion and EPN mostly consolidate, though some side with Morpheus, changing/expanding the suborg as people will it to be (i.e. if players wanted EPN to remain separate enough, there'd be 3, otherwise, they'd come together and there would be 2 - Zion/EPN and Morphite)
Morpheus reveals his plot to recover Neo. The Machines reveal that they feared him doing so was an attempt to disseminate and distribute the code of the one, which would give an invaluable advantage to Zion in the war.
Morpheus states that this is a continued goal, one which his group will strive to achieve.
He also starts looking into Sarah Edmontons.

Veil has enough of Cryptos's Machine-loving and slits his throat in the night. She threatens to kill any of her crew who disobey her or disagree with her action, and ends up killing a few more before winding up with a nasty scar and a room full of people who won't cross her.
Cypherites are split between Cryptos loyalists and Veil loyalists, both of whom are bitter rivals now.
A new character rises up as leader of the Cryptos loyalists. They do things a bit less violently, but with more dedication to protecting bluepills than to killing redpills.

The Merovingian uses what information he has from the Oligarchs he has been in contact with to start research on override routines, intending to make himself into an Oligarch.
Cryptos's research is abruptly ended when he dies, though the codes, still somewhat flawed, have already gone out.
Zion starts studying the unibody ship design and attempts to make contact with Halborn and Carlyne to further their research.
The Machines continue to target and attack Zion and EPN in the Real.
Morphites begin using code bombs and further research the power supply of the Machines.

I might've had some other stuff, but it's not in my notes and I probably forgot it.

[EDIT] Outcomes for the Sati battle:
Zion/EPN wins They use her to develop Oligarch abilities and raise her to be a new Oracle.
Morphites win: They use her to extract secrets of the Matrix's design and obtain Neo's location through her use. They then return her to Seraph and have her be raised as a new Oracle.
Machinists win: They have her design new encryption on the Matrix which prevents Oligarchs from jacking in, or, at the very least, from having any override codes when jacked in. They then raise her on their own to be a new Oracle, installing what programming they deem "necessary."
Cypherites (Veil-Aligned) win: They keep her on a floppy on the winning Cypherite ship, with acknowledgement given that this is the case. Further hovercraft battles may happen with an attempt to free her, however, the operative of that ship is in control of what happens to her. If they break the disk she's gone. They can also return her to the Matrix if they want to. Otherwise, if they are downed in a hovercraft battle, the winning side takes the disk.
Cypherites (Cryptos-Aligned) win: Sati is used to perfect anti-overrides 100% and is given back to Seraph to become a new Oracle.
Merovingian wins: The Merovingian uses Sati to perfect his oligarch routines and overrides, and becomes a program Oligarch, eventually using her to send more of his programs into the Real (but not himself). Persephone leads this group of Real-based programs, and possibly steals Sati to keep this going, creating a splinter group. Persephone then raises Sati as her successor and gives her a raising similar to one which would bring to be an Oracle.

/my2cents.