Im not very patient. I also am not much of writer. I could try to make this a detailed story filled with quotes and descriptions. Yet I just know I would run out of steam. I've seen too many fan works die like this. So the following is more a fun description of an act of combining two anime's into a single fan fic, written this way rather than as a full story.

Well, here we go...

Its a multiverse. Not an infinite one, mind you, but one with many, many universes. One of these is the universe of the Sword Art Online and Sword Art Online 2 anime shows.

But another is different. In it, the events of Sword Art Online that happen... are the first 14 episodes.

In this universe, after the events of the aincrad arc, all the surviving players wake up, including Asuna and Kiritio. There is no second game, nor Sugo. The two wake up, and are married in the real world relatively soon. With the help of supportive families, a curious government, and contacts from within the game grateful for how they saved them, they are able to set themselves up, doing well in the school setup to help the survivors and getting the work needed to get on their own feet.

Yet what of Yui?

Fortunately (or not depending on your perspective) something has been watching. Something from a universe of Madoka.

What was watching? Perhaps a sub-group of the incubators who realized what they were doing was wrong. Or another alien race of similar strength. Unable to see the future with perfect accuracy, they still were able to sense that this intelligent AI was key. That somehow, the vicious cycle their Earth was trapped in would be broken by her. That she would hold a key to salvation for millions.

So, in an instant one night, while her parents sleep, the data that was Yui is removed, granted a human body, and her memories surpressed. She was then worked into this new world. Worked in with a new identity...

Homura Akemi.

From there, the series Puella Magi Madoka Magica happens as we remember it. But when you become a goddess, you see things. And so Madoka sees both the events of the Rebellion movie (a possibility for the future) and Hormura's origin.

From this, she knows she must stop the incubators. But how? Especially when she cannot interact with her universe directly for the most part?

Fortunately, there is a multitude of different universes, including those she is able to interact with to varying degrees.

Thus Madoka begins her campaign. She assembles allies from across the multiverse, working with them to figure out how to weaken the dimensional barriers of her own universe enough for her to defeat the incubators. A series of adventures takes place, bringing together such disparate forces as Nanoha and heir friends and allies, Shinji, Asuka, and Aki (of the fanfic Eva: The Second Try), Ikki and Stella, Kirito and Asuna, and even Ryuko and a resurrected (thanks to Madoka) Senketsu.

As the plan nears completion, Madoka starts whispering to Homura in her dreams. First, its "dont trust kueybey". After a few nights, she is able to speak to her for but a moment, hugging her and apologizing, letting Homura know to a degree that she came from another universe, and begging her to tell Kueybey nothing of this. Then the dreams start to include images of Kirito and Asuna. Homura even begins to see strange events around Mitakihara city. Finally, Madoka and Homura are able to have one final conversation, where Madoka tells her the next day to destroy her soul gem to regain her memories and to be able to live a normal life with her birth parents, but that Madoka will be able to, through various ways, always be able to communicate with her.. The next day, as she, Mami, and Kyoko follow kueybey to the outskirts of the city to fight wraiths, Homura fist bumps kyoko and even hugs Mami. She then steps out in front, hearing many voices now, and smashes her soul gem. Thanks to the work she and her allies have been doing, Madoka is able to use this gap to strike at the incubators all at once, reducing their power and trapping them as merely intelligent animals on a far away planet in the third dimension.

Homura meanwhile goes through a psychological event where the memories of Yui, combined with contact with Madoka, effectively cause her to be reborn into the body of Ruiko of A Certain Scientific Railgun. Madoka brings her to the command ship of the alliance she forged, where Homura wakes up in the arms of Kirito and Asuna, and the three reunite. They decide to live in Kirito and Asuna's home universe, where they will be watched over by that universe's version of HYPNOS, formed after contact with Madoka to interact with her and the allies she forged. They will crossover from time to time to help one another. (Such as Ikki and Stella, for she is now queen of her nation, which has become a constitutional monarchical powerhouse thanks to technology gained from the travels. And Ikki is doing well as prince consort, having broken off ties with his dad after calling him on his cruel disregard for those not born lucky. After his dad died, he learns from his mother that his dad died full of regret for how he treated his son).

We see Homura, who now looks exactly like Ruiko of A Certain Scientific Railgun, befriending who appears this universe's (the universe of Kirito and Asuna) counterpart to Uiharu, who in fact is Aki, who thanks to the adventures, is now older, and has settled into this SAO universe with Shinji and Asuka. We then see Aki introduce her to Kuroko, though one very different from the show. In addition to there being none of the advanced science or magic of the "A Certain X" franchise, this Kuroko is MUCH more toned down. Shortly after the introduction, it comes out that Kuroko is frustrated and a little dejected, because while her groping habits don't exist here, her crush on Mikoto does. And shortly before this meeting, when Kuroko tested the waters by mentioning she could see herself in a relationship with a woman, Mikoto indicated she personally could not. We see Homura become friends with Kuroko, and even be introduced to Mikoto, with the group becoming friends and even being trusted enough to in time be introduced to Madoka herself (who while mostly speaking with Homura, has also explored what she thinks her role in this universe should be by helping HYPNOS make significant technological advances in secret).

Then one night, while Homura and Uikaru are shown setting up Kuroko on a date, we see Madoka talking to Mikoto, encouraging her to tell Toma how she feels. We are then treated to a scene of her running to find him, while Madoka and the spectral forms of Sayaka, Kyoko, and Mami are shown flying behind her while the opening song from the Rebellion movie plays. They even pick up Homura, whisking her away as they all gather to encourage (while staying invisible) Mikoto, who tracks down Toma, and after awkwardly trying to get the words out, pulls him in for a kiss.

The true end of this tale involves a montage, possibly set to the song that played at the very end of the last episode of Fullmetal Alchemist Brotherhood, where we see Toma and Mikoto walking down the street hand in hand, other other characters at peace, and a final shot of Homura, Madoka, Sayaka, Kyoko, and Mami sitting on a rooftop watching the moon.