Herein lies a series of ideas that failed to crystallize into even a full chapter's worth of material.
Title: Two Minds are Better Than One
Crossover: Code Geass and Death Note.
Summary: Some Code Geass characters exist in the Death Note world. Code, Geass, Brittania, Sakuradite, Knightmare Frames, the Thought Elevator, etc. do not exist, the only change is the presence of the new characters. Lelouch Lamperouge (his real name) is a French transfer student going to the same school as Light. His sister Nunnally was injured in the car accident that killed one of their parents (which one is left to the discretion of the author) permanently crippling her legs (blindness optional). Charles Lamperouge is/was a high-ranking executive in a company or an important political figure in France. Other characters are inserted where appropriate: Kaname Ohgi could be the cram school teacher, Kyoshirou Tohdoh could be a member of the Japanese police working with Soichiro Yagami, Jeremiah Gottwald could be a member of the FBI team with (or replacing) Raye Penbar. Code Geass characters can either replace or augment the Death Note cast at the author's discretion. No dimension hopping, portals, or other poor plot devices: the characters are born, raised, and live as normal; they just happen to share the name, appearance, and personality of the appropriate character from Code Geass.
Specifics: Lelouch will provide Light with a "straight man" second opinion and encourages restraint and caution that Light lacked in canon. For example, Lind L. Taylor will survive his on-screen appearance only to die a weak later under less suspicious circumstances (stabbed in a bar-fight, died in a car wreck caused by a mechanical failure, bad fugu, etc.). Lelouch can also take over as Kira if Light is under surveillance or doesn't remember himself (no "I'll take a potato chip, AND EAT IT!" scene necessary). Amane Misa is a singularly annoying character and I demand that she be replaced with either Kallen or C.C. both as the second Kira and as Light's love interest. The other can hook up with Lelouch. If, somehow, the plot lasts past the time-skip, Lelouch will have returned to France and formed the Black Knights, a militant pro-Kira terrorist group, which he leads as the enigmatic masked figure Zero.
Title: Naruto Xavier
Crossover: Naruto and X-Men (Days of Future Past Movie)
Summary: An incident with Blink during the conversation between young and old Charles Xaviers casts the elder's soul adrift into the multiverse. Meanwhile, after a very ruthless "Fox Hunt", Naruto's admittance to the hospital, and a nurse administering a strong neurotoxin instead of his painkiller; Naruto is found brain-dead. Charles inserts himself into the empty mind of Naruto and wakes up (much like he does in the stinger ending of X-Men 3) retaining his telepathic powers in addition to the new ninja skills. Now effectively an overpowered Yaminaka, a genjitsu specialist, a sensor, a jinchuuriki, and having the decades of experience of Charles' life; Naruto takes the ninja world by storm.
Specifics: Xavier's powerful telepathy allows him to emulate or exceed the abilities of a number of techniques and kekkei genkai in the ninja world. The ability to enter, read, and alter someones mind up to and including mind-controlling them is on-par with upper end Yaminaka techniques without the obvious weaknesses of having to leave his own body behind or only messing with one mind at once. As an extension of the previous ability, Charles can make the victim(s) perceive something other than reality, an illusion. Unlike genjitsu, this ability affects the mind directly without bothering the chakra network meaning they cannot be detected or dispelled like genjitsu. His ability to stop the perception of time for everyone in an area will certainly come in handy as well. He is able to detect the thoughts of everyone within a wide range of himself (250 miles according to the Wiki), this acts as a very powerful sensory ability. Finally, none of these abilities would use chakra (not that he would feel the drain if they did) preventing them from being felt by chakra sensors and allowing him to continue using them if his chakra were sealed or disrupted in any way.
In addition to his powers, Xavier bring a large amount of intelligence, knowledge, and experience with him. His mental faculties are beyond genius-level including eidetic memory and a penchant for strategy. He has earned numerous doctorates (Anthropology, Genetics, Bio-Physics, Psychology, and Psychiatry at least). Prior to the injury that rendered him paraplegic, Xavier was apparently an accomplished martial artist specializing in non-lethal take downs and pressure points; his mind-reading would aid him in anticipating his opponents moves as well. Finally, the experience of running both a school for super-powered youngsters and an underground paramilitary organization for decades will serve him well as either Hokage and/or Uzumaki clan-head.
Notes: The Naruto-verse runs on secrets. All of the dramatic tension in the entire series is based on who knows what and when, who is keeping secrets and from whom, and people performing actions and gaining intelligence without other people knowing. Throwing a character into this world that you literally can't keep secrets from is completely broken. For one, Danzo will be within his range from the moment Charles becomes Naruto and he has his hands dirty with events running right up to the final fight in canon. Breaking that Pandora's Box open at the beginning of the story will basically eliminate any challenge and dramatic tension from Naruto's entire life. I expect this story to be short, cracky, and Naruto to be a massive Stu.
Title: Private Server: Brockton Bay
Crossover: Matrix and Worm
I was thinking about a crossover idea for Worm, but wasn't sure where to start, So I started doing some free-associating. There are some consistent themes and undertones running through a lot of Worm fanfics which grabbed me: "Powers are bullshit.", "Tinkers are bullshit.", "That shouldn't work.", "That should be impossible.", etc. I started thinking about other forms of media where "It just works." is an acceptable explanation. Not some pseudoscience technobabble that tries to explain why something works, but where they actually present an impossible situation and it behaves under an impossible set of rules and it just works. I came up with only one good answer:
Video games and computer simulations.
Alright, step one complete, we are approaching the Worm-verse as a game or sim and rolling with that logic. Powers are essentially cheat codes, allowing the user to perform feats outside the possibility of physics. Powers don't break physics because there is no physics to break: only what the computer says is true. Similarly, the "black-box" tinkertech isn't actually super advanced, it just *looks* that way to an outside observer and then functions the way the sim tells it to. Now what source materials include a simulation of reality indistinguishable from the truth as a plot device? SAO? Too happy, not big enough. .Hack? Not familiar. Overlord? Not really applicable without a major overhaul. Then it hit me:
Perfect: step two complete, we have our crossover. What springs to mind is this: the machines need to learn how to fight humans that are gaining control over the system in the Matrix, gaining superpowers basically. How would a Machine learn how to fight a human with superpowers? By watching other humans fight humans with superpowers in a controlled environment and taking notes. The machines split off shards of the Matrix, isolate the networking physically from the Matrix at large, and give a small sub-set of the population ways to cheat: "Powers." As a social experiment on a massive scale, the machines *want* conflict to happen between the owners of the cheats so they do everything in their power to make sure it does. The Endbringers, The Butcher, Coil, certain other villains, and that little itch all capes get that makes them want to fight all contribute to this. The machines then observe the fighting that takes place, take notes, and adapt their Agents' abilities and strategies to emulate the best performing groups.
Excellent, step 3 complete, we have our deep background. Now we need the setup for the actual story. After the events of Matrix Revolutions, Deus Ex Machina attempts to honor Its deal with Neo: humans are free to stay in or leave the Matrix as they please. However, some of the experimental "Private Servers" are not responding and their people are effectively trapped until It can reestablish contact with those servers' system administrators. In the Matrix proper, the sysadmins were named The Architect and The Oracle. In the Worm-Matrix, the sysadmins are named The Thinker and The Warrior. The Thinker focuses on analyzing the Capes overall stratagems: power synergies, logistics, big-picture stuff. The Warrior would be noting more specific tactics and combat methods on the small scale: hand-to-hand techniques, marksmanship, when and how to transition between the two. They were analyzing how these things change when one or more sides in the conflict have "above normal" capabilities. Neither have responded to network queries in some time. Deus enlists the assistance of Neo to help resolve this situation. Now, canonically, Neo died when Deus flooded the Source through Neo as Agent Smith was assimilating him, here we can assume he survived that somehow. A blatant hand-wave perhaps, but necessary. The opening scene of the story would be Neo and several Agents walking down a long, white, door-filled hallway while one of the agents briefs Neo on the world he is about to enter.
Step 4 down: story setup complete, moving on to the story plot. Early on in the Worm-Matrices existence, a group of rebels managed to kill The Thinker and cripple the function of The Warrior, rendering him nearly brain-dead. This cut-off most of the Private Server's command and control and completely severed any ability for the outside world to affect the system. This group would eventually call itself Cauldron. Neo's objectives are to restore both sysadmins to function so that Deus can shut down the server and prevent Cauldron from acting before that happens. His assets include several Agents going in with him and the Machine assets in place: Coil, The Butcher, Jack Slash, and several other villains/rogues who have done little but incite conflict and provoke response. The Endbringers can be turned off and on, but not controlled in any meaningful way.
I kinda like the idea that the villains are the allies in this one and the normal "good guys" are the antagonists, throws expectations on their heads. The one big funny moment that springs to mind is Neo bumping into PRT trouble and getting into a fight with Armsmaster and Miss Militia. Neo proceeds to take the "one-handed and I'm not even looking at you" defense from the end of the first movie and uses it on Halbeard, then raises his hand at Hannah and says "no" to a full magazine-worth of assault rifle bullets. TFW: O_o Also: the baseline setup could be used for any number of Matrix crossovers as well; just change the admins, the agents-in-place, and antagonists to work with the new world that Neo is being dropped into.