Twi’s intentional ripping open portals let a lot in. Magic grows on itself, and the world is slowly building to become a magical world like Equestria. But it’s a world unused to magic, and since the world took a different path, the magic will be different than the magic in Equestria. So Twilight and Sunset head off to study how magic works and help out where it’s causing trouble. If creatures are around and they can’t handle it on their own, they can call the other five to come help, but they keep getting better. Eventually the two of them realize they’ve taken on a creature that previously they would have called for backup. This makes them realize they’re getting adept at using the magic that’s becoming more abundant.
After one particularly exciting magical experiment, studying something, Twilight gets over-excited. In her enthusiasm, she grabs Sunset’s face and kisses her square on the mouth. She turns to go grab something to help measure whatever it is they’re doing when she realizes what she had just done. Suddenly her attraction to the other girl is out in the open. She turns back, cringing at what she’s sure will be flat rejection. But Sunset is mostly still stunned. With a shake, she returns to the living and looks at Twilight. “I was…not expecting that.” When Twilight starts to apologize and looking like she wants to run, Sunset calms her. Tells her she’s not mad. “Let’s finish up here, get our measurements, clean up, and let’s go back to the hotel. We need to talk about this.” There’s tension as they pack things up, though Sunset tries to reassure her she’s not mad.
They get back to the hotel and order a pizza (Sunset’s still a little wary of eating meat, but found her human body doesn’t mind it as much as she was expecting). Then they settle in to talk. Sunset asks Twilight how long she’s been interested in her. Twilight shyly admits it started pretty much immediately after Sunset saved her from her evil self. Sunset’s eyes go wide. “Really? You’ve been holding this in for five years? You could have said something! I wasn’t going to hate you.”
“Well, I’d heard you had a boyfriend at one point. I didn’t think you’d be interested.”
“You mean Flash Sentry? At the time, I was using him to gain popularity, and I broke up with him when I got it. I was never romantically interested in him. To be honest, I haven’t thought about anypony romantically in….I’m not sure how long.”
“So you still wouldn’t be interested in me.”
“I didn’t say that. I’ve just been so focused on other things that romance didn’t even enter my brain. You’re my best friend, Twilight. I think I’d like to try it, if you don’t mind me not knowing what I’m doing.” Twilight chuckles awkwardly.
“You wouldn’t be the only one. I’m like you a little. Never considered the possibility until…until it happened.”
Sunset places her hand on Twilight’s and gives it a squeeze. Smiling but unsure, she leans over and places a kiss on Twilight’s cheek before leaning up against her more solidly. They spend the night going over the results of the day, eventually falling asleep covered in paper and leaning together.
Not much changes at first, but they keep finding and exploring magical anomalies. They occasionally pony up when they’re at their most magical, but a lot of their down time is just spending it together. They’re more intimate and slowly become a cute little couple.
The strangest thing they come across is a portal, sort of. It’s more just a crack, but it definitely goes to Equestria. They reason it must be a leftover from Twilight’s rampage. They test the flow of magic before deciding to seal it before it can do any damage. However, immediately after they’ve finished a person runs up to them screaming.
“No, no no no no! Why did you do that? How am I supposed to go home?” After calming down themselves, they manage to calm her enough that she can explain fully. Turns out she’s a pony. She was exploring near her home and fell through this crack. After reassuring herself despite her strange new form, she’d gone exploring with the assumption she’d be able to slip back through to go home. Now that possibility was gone.
“Well, if it’s any consolation, you wouldn’t have been able to go back through. This world has a dearth of magic, so it was flowing from Equestria, making it a one way road.” Sunset explains. This, however, does not really offer much consolation. Fortunately, Sunset and Twilight know another way back to Equestria. They invite her back with them, befriending her on their trip back across the country, and encountering a few more magical things.
A few days before they arrive Sunset pulls out a beat up journal. It’s been a long time since she’s spoken regularly with Princess Twilight Sparkle. She sends and opening message to see if Twilight has time to talk. The response is almost immediate, as though the Princess had been waiting for a message. Sunset explains the situation and asks if Twilight could take the mare back so she could get home. Twilight agrees but wants to know more about what Sunset has been doing for so long.
Sunset explains about finding her place in the world by following the magic and exploring it. She details some of what they’ve found, and her handwriting gives away that she’s rather excited about it. Twilight mentions that in those intervening years, the portal through the mirror had opened naturally. Sunset could have come back to Equestria if she’d wanted.
Sunset is quick to dismiss this. She’s found a home here, she’s happy. She admits though that when the time came she watched a clock the entire day, just in case she felt tempted. When the time was up, she sighed in relief. Relief! She hadn’t wanted to go back and had been worried she’d feel some betraying thoughts of returning.
Twilight says that since the mirror was going to be opening soon on its own again, if she could come to visit for a while. Sunset agrees, she’d like to show the Princess their research.
They arrive in time and the mare is sent on her way, with travel taken care of so she can get home without worrying anypony any longer. Twilight was to return and meet Sunset at Sugarcube Corner to talk. Sunset tried to get Sci-Twi to come, but she felt awkward about meeting her other self again. And she was going to be meeting her brother and sister-in-law for lunch anyway, and there was definitely no other reason she could possibly be feeling uncomfortable.
Sunset just waited. They’d gotten to the point where they could talk about pretty much anything, but sometimes Twi just needed to build herself up first. Finally she nervously made eye contact with Sunset.
“To be honest, I’m a little worried. You’re going to talk to me in there, and I’m feeling…jealous? I’m kind of worried you’ll like that version of me better and go back with her to Equestria.” This was not what Sunset had been expecting. She placed a reassuring hand on Twi’s cheek.
“The thing is, she’s not you. I don’t care that you have the same name, or that you look almost identical. You are not the same person. You’ve had different life experiences and different memories.”
“Yeah, but what if – “ Sunset shushed her with a finger to Twi’s lips.
“I have spent the last five years with you. That’s five years of experience, and five years of memories of you. I don’t have those memories with her. I certainly don’t love her, as I love you. The reason I love you is because of the things we’ve done together. I’m with you and that’s how I want it to stay, this other Twilight won’t change that.”
Greatly reassured, Twilight kisses her deeply for a moment. They’d had this conversation just outside Sugarcube Corner because Sunset was supposed to meet Princess Twilight there soon. Unknown to either of them, that Twilight had arrived early and had nearly walked around the corner on them, only stopping short to listen first. So, yeah, she hears everything about them dating, but to avoid bumping into either one of them and letting them know she found out, she sneaks around and enters through the back, sitting at a table just before Sunset Shimmer walks in.
She manages to keep her cool and Sunset shares the data from the experiments, which distracts her for a good long time, but eventually they start talking about what they’ve been doing and Twilight can barely contain herself. She finally bursts during a lull in conversation.
“So, how long have you been dating other me?” Sunset is quite surprised by this question, but quickly catches on.
“You saw us outside, didn’t you?”
“I didn’t want to intrude, but it was a little weird seeing my face being kissed by you.”
And now Sunset has the unfortunate duty of restating that they’re not the same person. After what is essentially a small argument about how weird it is to be talking to an alternate of the person you’re dating, they fall back into an awkward silence. Twilight fills the void.
“I heard you say you love her. Is that true?”
Sunset nods and smiles sweetly. “I really do. I didn’t expect it to happen, but it grew on me so easily. She’s also the reason why I never really felt drawn to return to Equestria. I want to be with her.”
Twilight smiles awkward. “Well, I can’t say it’s not strange, but if it makes you happy, I’m glad you’ve found her. Congratulations!” Sunset’s smile is relieved and conversation after that is easier.
They spend a few more hours catching up before Twilight announces that she has to leave. She made plans to see the others before she left, and she doesn’t have much time. The Portal isn’t as much of a barrier any more, but she’s got duties to attend to at home. They say their goodbyes and Sunset goes to meet her Twilight, each step lighter than the last.