20 years ago:
Twilight is in the caverns under Canterlot castle, discovering the real Mi Amore Cadenza. In the meantime Queen Chrysalis is disguised as Cadence and is going to marry her older brother. Twilight and Cadence are about to reach the entrance to the cavern, but are stopped by a group of changelings who disguised themselves as the royal guards.
"Cadence, you go on ahead, I'll take them on," Twilight demands.
"Are you sure Twilight?" Cadence asks.
"I'm sure," Twilight answers.
Cadence hesitates at first, but then nods her head and escapes the caverns, while Twilight
fights the changeling on her own. Twilight fight the changelings as hard as she could, but she used a lot of her magic, and her being out numbered, she is easily defeated and got beaten up until she got unconscious.
The changeling soldiers decide to get rid of Twilight before any pony gets suspicious and guesses where they are. They go to some kind of gate with a strange star shaped symbol on it. It wasn't long until Twilight regains consciousness a little and sees the gate, and it didn't take long for her to realize what the changelings are going to do to her. Twilight tries to get out of the changelings' grasps, but she was too weak from the fight to escape. The changelings are able to throw her through the gate and it close right behind her when she reaches the other side. At the other side of the portal Twilight tries her best to get back to Equestria, but at the beginning of sunset the portal close. Twilight was so weakened from the fight that she pass out with no way to know where she currently at.
On the beach of Okinawa, Seiichiro Hinata, a 16-year-old boy, is riding his bike home from doing errands for his mother. He was riding past the beach until he sees a glowing light and decides to go check it out. When he got there, the light disappears in front of him and he sees a girl with indigo hair and a magenta and light purple streak in it. She even has a magenta 6-pointed star with 5 small white 6-pointed stars on her right cheek. She is also wearing a lavender dress. When he got a closer look at her, he sees that she was beaten up and have bruises, cuts, possibly broken bones and a concussion. He uses his cell phone to call an ambulance.
"Hello ambulance, I found a girl on the beach with bruises and cuts, and possibly a concussion and broken bones. This is Seiichiro Hinata." It didn't take long for the ambulance to get to their location. While the ambulance is on their way to the beach, he decides to call his parents to tell them what happened.
Back in Canterlot, Equestria:
The changelings along with their queen are defeated by Shining Armor and Princess Cadence's love for each other. (True love conquers all)
Princess Celestia comes up to the ponies and says, "Now that the changelings are defeated, we can get the real wedding ready."
Every pony agrees to the idea, but Shining Armor notices that some pony is missing. "Hey, where's Twilight?"
Every pony now notices that Twilight is not here, until Cadence remembers, "Twilight is still at the caverns where I was trapped."
Princess Cadence leads them all to the cavern. When they got there, the light that Twilight saw earlier has disappeared and it also seems that Twilight has disappeared without a trace.
"Princess, are you sure she is down here?" Rainbow Dash asks.
Princess Celestia's eyes widen and notice the symbol, "It can't be!" Princess Celestia seems to know what the gate is: "The gate of Zanes."
"Who, the what now?" Applejack asks.
"Meddle Brook made this portal thousands of years ago, so that he could travel to another world. But the portal can only be open for 7 days every 20 years," Princess Celestia replies.
"20 years," Every pony says with a shock.
"I heard from the changelings and the queen that they were going to send me to the other world, if that's true then…" Cadence starts to cry, while Shining Armor and the others refuse to believe that such a misfortune had come to one pony.
Rainbow Dash shouts, "Search the caverns again, she must be hiding somewhere!"
"I'm afraid that the deed is already done; I just used a detection spell and the only source of life here is ours," Celestia starts to cry, "I'm afraid Twilight Sparkle is lost to us."
Every pony is silent and heartbroken. Especially Shining Armor; he believes that it was his fault that this happened to his little sister. Then Celestia speaks up, "I think we should postpone the wedding." There are no arguments to that statement and they decide to leave the caverns and hope that their friend is ok.
In one of Okinawa's hospitals Twilight Sparkle regains consciousness and notices that she is in an unfamiliar room. She also notices that her body is different than normal. She wanted to scream but couldn't. Then Seiichiro comes in with a bouquet of lilacs with baby's breath, "Hello, I'm glad you're alright. When I found you, you were hurt pretty badly and had some broken bones, but they will heal in time. By the way, I'm Seiichiro Hinata, what's your name?"
Twilight hesitates at first and then finally says, "My name is Twilight Sparkle."
Twilight explains to Seiichiro what happened to her. He notices the look from Twilights' eyes that she is telling the truth, but he decides that it would be a secret between the two of them. When she got out of the hospital, Seiichiro decides to teach Twilight the ways of his home world. It was difficult at first, but with Twilight's intelligence she was able to prosper just fine. Seiichiro thought it would be a good idea to change her name so the people wouldn't get suspicious. He decided to call her Yugure Kudo.
When summer ended Seiichiro decides to enroll Twilight in the school he was attending, and it wasn't long for love to blossom between the two of them and then they started dating. When they got to college Seiichiro proposes to Twilight and she accepts. Then two years later during their college years they got married and still work hard with their schoolwork. After graduation Twilight becomes a school teacher while Seiichiro becomes a game designer. They had a good life until on the 5th year of Twilight's life in Japan, she and Seiichiro have a wonderful blessing. Twilight becomes pregnant, and on July 1st she gives birth to a baby girl. She has Twilight's indigo hair, eye color and magenta streak, but the other streak is pink strip next to the magenta streak. Seiichiro comes into the room with a bouquet of roses and baby's breath for Twilight and their new daughter.
"She's beautiful," Twilight says.
"Yes she is when are you going to tell her?" Seiichiro replies.
"About my family heritage," Twilight says and Seiichiro nods his head. Twilight says, "I don't know, I was hoping to wait until she is older."
"You know, the longer you wait the harder it is to tell her," Seiichiro replies, and she knew that he is right, but decides to change the subject.
"So, what do you think we should name our daughter?" Twilight asks.
"Well, since the cherry blossom trees are blooming so beautifully, I think we should call her Sakura," Seiichiro comments and Twilight thinks the name is perfect.
"I love it, welcome my little Sakura," Twilight says beautifully.