If there was something that Twilight and Spike were expecting when they walked into the map room, it definitely wasn't Starlight Glimmer waiting for them to exact some kind of revenge.
"Welcome home, Twilight!" Starlight Glimmer said before casting some sort of spell on the cutie map. Twilight stuck out a wing to shield Spike from whatever damage this unknown spell could do. While it would be remarkably easy to knock out Starlight Glimmer right then and there, Twilight liked to leave violence as a last resort.
In a move that Twilight would only describe as "incredibly stupid," Starlight tossed the paper containing the instructions to cast the spell behind her, as if she would no longer need it. "Won't be needing this anymore!"
Twilight stood her ground, waiting to see what kind of offensive spell Starlight had decided to throw at her. She was surprised when a dome made of magic appeared above the map, which promptly sucked Starlight up into it. Once everything seemed quiet, she brought the paper to her face to give it a read.
"Time magic?" She gasped in horror, before narrowing her eyes. "What's she trying to do?"
"Maybe she's going to the past to kill you as a baby?" Spike suggested.
"That seems a bit extreme," Twilight said. "You stay here, I'm going to go after her and see what she's up to."
"But wouldn't it make more sense for me to come with and help you out?" Spike asked.
"Very funny Spike, but I'm not bringing a child into the past with a dangerous unicorn who hates us. Go over to Rarity's house and wait there until I come get you."
Spike looked very concerned upon hearing this. "But what if you-"
"I'll be careful, and besides, there's not much she could do to an alicorn," Twilight said, flaring out her wings to make a point. "I promise I won't do anything stupid, and I'll make doubly sure Starlight Glimmer doesn't do anything stupid either."
Spike looked a bit skeptical, but tentatively agreed to this course of action. "I know you've said you'll be careful, but can you make it a Pinkie promise?"
"Cross my heart, hope to fly, stick a cupcake in my eye," Twilight recited. "I'll be careful, Spike, you don't need to worry about me." The two shared a hug before Twilight cast the spell on the paper, following Starlight into the past.
Twilight emerged from the dome high above the ground. She assessed her surroundings, determining herself to be somewhere in Cloudsdale. Finding a secluded spot to land, she stood on a small cloud that was further from many of the others. She couldn't see Starlight anywhere, and hoped the unicorn hadn't fallen through the clouds and died. While looking around, she spotted a light blue filly with a rainbow mane. She figured that it must be Rainbow dash, and judging by the fact that Rainbow didn't appear to have a cutie mark, Twilight concluded that she was at least 20 years in the past, possibly further.
Leaping to a cloud a bit lower, Twilight scanned her surroundings to try to catch a glimpse of Starlight. With any luck, she'd be able to pluck her from the past and be back to the present before anyone even noticed anything was amiss. Luckily, being in Cloudsdale, it was rather obvious where Starlight was when she saw magic nearby.
Twilight's eyes widened when she realized just exactly what Starlight's plan was, spreading her wings to put an end to the deranged unicorn's scheme.
"What did you do?" Twilight shrieked. "Let Rainbow Dash go!"
"You are about to find out" Starlight replied ominously.
Twilight rolled her eyes. It was just typical that Starlight would fancy herself some sort of mysterious and powerful force of nature. Twilight was about to respond, when Starlight cast the time spell again.
"See you soon!" Starlight taunted as Twilight was sucked into the magic dome again.
Twilight awoke to find herself sitting at the cutie map. This wasn't unusual, as she held many a late night here with either a good friend or a good book. The unusual thing about this time was that the castle was gone, as was much of Ponyville. The entire area seemed a bit devoid of much of any life.
Getting a bearing on her surroundings, she started to head towards the center of Ponyville in hopes of finding some information. On the way, she decided it would be a good idea to keep a low profile, and headed instead for Sweet Apple Acres. If Ponyville was here, she reasoned, Sweet Apple Acres must also be here, given the Apply family's role in the founding of the town.
Twilight was quite unnerved upon arriving at the farm. If she was being honest with herself, she couldn't even call it much of a farm anymore. There were industrial machines all over the place, producing what she assumed was apple sauce in high quantities. Spying a familiar orange pony, Twilight trotted up to Applejack.
"Applejack? Is that you?" Twilight asked.
Applejack didn't turn from her work. "Yup, who else would it be?"
Twilight couldn't think of a good response in this situation, and fell back on a good conversational staple. "Anything new happen lately?"
"Nope, just continuing to do my part for the war effort," Applejack replied nonchalantly, still not looking Twilight's direction. "Do I know you?"
Collecting her jaw from the ground, Twilight gathered her thoughts before proceeding. "I'm... not from around here. Did you say something about a war?"
This finally got Applejack's attention. Turning to face Twilight, she said "You aren't seriously going to tell me you don't know about the war." Seeing the sheepish look on Twilight's face, she continued "the war against King Sombra?"
"WHAT?" Twilight shouted.
"Where have you been? This thing's been going on for years at this point. Do you need medical attention or something?" Applejack asked.
"Uhh, no. I'll just be on my way." Twilight said before turning and galloping away.
"Huh, what a weird pony." Applejack mused before turning back to her work.
Twilight was frantically making her way back to the map. It was rather obvious what Starlight had done. She interrupted the sonic rainboom that had been the catalyst for all of her friends getting their cutie marks. This was simultaneously very stupid and very petty. Twilight didn't think that this would be the direct result of her and her friends dismantling Starlight's little cult. This seemed a bit too extreme for that. There had to be some underlying issue that had driver the unicorn over the edge of sanity.
Upon arriving back at the map, Twilight resolved that there would be no time shenanigans, and that she would stop Starlight in her tracks immediately upon arriving back in the past, and cast the time spell once again.