Code Geass: Nightmare Of Nunnally is an Alternate Universe version of the original Code Geass. The story starts off the same way as the original right up until Lelouch first meets C.C. From there, Lelouch and C.C. are (presumably) killed in a nearby explosion. Nunnally, after hearing news of the explosion, heads over to the area and finds a strange doll with a Geass symbol on it. It speaks to Nunnally telling her that it's a "keepsake from her brother" and convinces Nunnally to make a Geass contract. She does, transforming herself into an Action Girl and gains the ability to see into the future, along with a katana wielding, EVAexpy Knightmare Frame.Enter a new group of Britannian agents, the "Britannian Special Honorary Foreign Legion Irregulars"; and some shiny new powerups for others.
Code Geass: Nightmare of Nunnally contains examples of:
Action Girl: Nunnally, as well as Alice and the Irregulars. And Anya ( channeling Marianne).
Bad Ass: Zero. Seriously, this version of him is so awesome, he fights Knightmares on foot.
And he can stop bullets by posing!
In the last parts of the manga, The Knights of the Round show that they can do the same thing.
Heck, C.C. is Bad Ass. And not only because she is part of Zero here - she did some action in flashback to the Hundred Years War.
Bad Ass Normal: Suzaku. All from above have superpowers. He doesn't need them.
Badass Long Coat: Used a visual cue for Alice's transformation into Nunnaly's knight. In the previous scene she wore her uniform in a cell and emotional wreck. In the next scene she's tall, proud, and wearing the long coat.
Bittersweet Ending: The world is saved from Charles and Marianne's Assimilation Plot and Euphemia abolishes the Pax Britannia and the other countries establish independence, but hatred in Britannia hasn't quelled and it's still enemies with most of the world (possibly barring Japan) and Lelouch spreads chaos and Geass because that is his role.
The Void apparently wants to suck reality back into itself; so it uses the Demon King to war and cause Geass to make mankind destroy itself. Nunnally says she believes that an immortal Lelouch will eventually be able to bring true peace to the world; but Lelouch feels that he will forever be the Demon King; trying to destroy it.
Bodyguard Crush: Alice really doesn't hide this at all. She wants to be Nunnally's Knight, even if she has to crush the rebellion and that strange new Knightmare that has shown up.
Nemo: A cloned doll of CC; she connects to Nunnally early on and becomes her Super-Powered Evil Side (although nobody can see her "Dark Nunnally" aspect) and later after Nunnally rejects her; she gives her power to Alice.
The Irregulars: A group of mech-riding war orphan girls trained as Britannian Agents and given artificial Geass powers; they are under the command of cyborg scientist named Madd.
Alice is one of them. She has Super Speed. She's also a fellow student of Nunnally's and her good friend; but doesn't realize she's fighting Nunnally on the battlefield; while fighting for her sake. (A common Code Geass theme)
Demoted to Extra: Between Nunnally, the Irregulars, a single "season", and long flashbacks, a lot of characters have their parts reduced dramatically. Poor Orange-Kun gets the worst of it, his role consists of getting his shit wrecked by NUNNALLY, than again by NAMELESS MOOKS. That's it.
Cornellia only faces superpowered enemies and has to be resqued by Suzaku twice. Same for Kallen - she only wrecks a few mooks, gets outmatched by Nunnaly in the second battle and stalled against zombie mechas in the finale.
Enemy Without: Nemo chooses to take Nunnally's sublimated anger and hatred as her power source. The problem; though, is that it's NUNNALLY and this is in a limited supply. Nunnally eventually breaks the contract; though she reabsorbs Nemo on her terms in the end.
Fan Disservice: We see Nunnally being subjected to several Panty Shots in a early chapter. It is not portrayed in any sexual sense, considering that Nunnally is a crippled blind 14 old girl. If anything, it ruins the mood of the scene.
Fix Fic: Euphemia gets a serious raw deal in the main series: she nearly ends the rebellion (and the series) by creating an independent Japan within the empire and even convinces Lelouch to side up with her, until Lelouch's geass freaks out at the worst possible time and forces her to kill every Japanese at the signing ceremony. Nightmare manages to pay her back just about everything she's due by giving her a fat pile of Big Damn Heroes moments, and eventually crowning her Empress of Britannia.
Gambit Pileup: The last volume of the manga involves Charles trying to complete his Assimilation Plot while Marianne plans for Nunnally to go to Kamine Island, Rolo trying to get Nunnally's code to become Demon King, Schniezel's plan to install Euphemia to prevent the Assimilation Plot, Alice trying to save Nunnally and the combined forces of Japan and Britannia working to stop Charles.
Lady and Knight: Nemo claims to be Nunnaly's knight at the end of the first volume, though they fight together. After Nunnaly breaks their contract and is captured by the Order of Eden Vital Alice takes up the mantle and the trop is played straight: Nunnaly as the Bright Lady (good natured, princess etc) and Alice as the Bright Knight (powerful, devoted to the lady, fights for her sake). At the end of Volume 5, Nunnally asks Alice to be her official knight and she accepts.
Large Ham: Lelouch, of course. Also, his 'twin' Rolo is one, posing magnificiently even as he boasts about his plans to kill Nunnally and Lelouch. Like big brother, like clone.
Les Yay: Alice adores Nunnally; and flat out tells her that she loves her in the end. This makes Nunnally change her mind regarding her father and mother's plan. There's also the canon Les Yay that Cornelia felt towards her half-sister Euphie...
Lighter and Softer: The cast and even the extras suffer FAR less physical and mental damage than the regular Code Geass. Even the villains are significantly more sympathetic and less monstrous. Exceptions are limited to C.C. and Genbu. Also, the knights of the round are all zombies, but its unknown if they are even the same knights. Moreover, take a note at Fix Fic above.
The Knight of One is still called Bismarck Waldstein, even though he really doesn't look it.
Living with the Villain: Alice and Nunnally go to school together, despite being the pilot of the Mark Nemo and a Britannian soldier, respectively. They find out about each other's identity in Volume 4.
Loving a Shadow: Alice worries that she's doing this with Nunnally, and strives to grow past it.
Meaningful Name: Nunnally's alter-ego: "Nemo" means no man or no one, which compliments her brother's alias "Zero" (as Diethard put it: Zero? As in... nothing?).
The Mole: Alice as a Britannian Agent; however she never betrayed Nunnally intentionally.
Samurai: Suzaku, very visibly. Aside from the armor on his uniform, he uses a katana.
Shoot the Dog: C.C. kills Genbu before he can kill Lelouch so Nunnally won't have to. ("I can't let the hands of Marianne's daughter become soiled").
Later on, Lelouch does the same for Nunnally for both Clovis AND the JLF hostage takers. Thanks to this, ejection pods and Karmic Death for Rolo and (sort of) Emperor & Marianne, Nunnally manages to end the series with a killcount of 0, despite piloting a humongous mecha in a gritty setting.
Shut Up, Hannibal!: Alice to Mao. "I have no idea what you're talking about. From my point of view... you're nothing but a murderer who tried to take Nunnally's life."
Start of Darkness: Charles was nearly killed in an assassination attempt on his idealistic emperor father, and survived with "The Dead" Geass. He uses it to regain power, and starts coming back to his previous ideals, but when Marianne is killed, it destroys her trust in people, and her surviving death with "The Soul" enables her to figure out how to access Eden Vital. We see in this in a chapter long flashback.
Succession Crisis: Surprisingly averted. After many nobles revolt when Charles initiates his plan, it is feared that any of them might try to take power in the confusion, while Cornelia and the Japanese think that they must be rallied together to fight Charles. They try to have Euphemia succeed, but they apparently need a majority vote for her succession to be recognized, then it is revealed that Schneizel and all those that rallied behind him, support Euphemia's rise to power.
Crazy-Prepared: Schneizel had all the paper work done before Charles initiated his plan. In other words, he was prepared for the emperor to overthrow his own government. All Euphemia had to do was accept the duty.
Super Strength: Dalque's Geass, "The Power," although she's apparently quite strong on her own.
True Companions: The irregulars who see each other as sisters. and betray her boss to save Alice.
Tsundere: Alice is a very mild Type A to anyone but those who she sees as a threat to Nunnally, when she becomes more violent. See Exhibit A
Was It All a Lie?: When Nunnally is captured by Britannia and asks Alice this, regarding her recent realization that Alice is a Britannian soldier.
Worf Effect: Suzaku, who was a Boring Invincible Hero in the original show. He gets the crap beaten out of him by Lelouch (who is on foot, but also in Powered Armor, at the time), turning the tide only for Nunnally to rip him a new one. He also fares poorly against Anya. The only fight he wins definitively is a showcase fight against Darlton, or when going up against mooks.
Lelouch(who was on foot), Anya, and NUNNALLY, though he is able to turn the tide in the first one. Unfortunately, that's still about 3/4s of the fights he gets into.