A young pony named Skeedaddle happily races through town to look for the Crusaders, finding that they're at Scootaloo's home, being watched by Scootaloo's Aunt Holiday and Auntie Lofty. Skeedaddle is pleased to show the trio he got his cutie mark in knot making, all which stemmed from ideas the Crusaders had given him. As he leaves, Scootaloo's aunts comment on the success of the Crusaders, but then realize they will be late for their train home for the weekend. Just after her aunts leave, Scootaloo gets a postcard informing her that her parents are coming home.
Scootaloo is far too excited at school the next day to pay attention, singing the praises of her parents who have important jobs in Equestria, studying exotic wildlife to find new medicines and remedies for ponies. Suddenly, a cragodile bursts into the classroom. Amid the chaos, Scootaloo's parents - Snap Shutter and Mane Allgood - subdue the creature quickly and apologize for the commotion. Scootaloo is thrilled to see them, and Cheerilee lets class out early. Snap and Mane decide to take Scootaloo and her friends out for a sundae. They spend time catching up on recent events, and Scootaloo wonders how long they'll be in town. Her parents reveal that they have new jobs in a more exotic location, where they can live together as a family, and they're only here for the weekend to retrieve their belongings, sell the house, and take the train to their new home... with Scootaloo. The Crusaders realize this will break up their friendship, but Scootaloo's parents insist she can still visit Ponyville, or vice versa.
Back at their treehouse, the Crusaders cry, not wanting to let their friendship go. Rainbow Dash arrives, having tickets to give them for the next Wonderbolts show. Upon hearing the Crusaders crying, Rainbow tells them they should never give up and try to keep their friendship together. Inspired, the three try a few schemes over the next few days to have her parents decide to stay in Ponyville, but they're committed to moving. Not wanting to go, Scootaloo prepares to run away to live with her aunts, and Apple Bloom and Sweetie Belle decide to join her.
At her aunts' home, the pair are happy to see Scootaloo and were unaware of her parents returning, due to a mixup in the mail. They express the same concern about breaking up the Crusaders, knowing that they have helped a lot of ponies in town and around. The next day, with the train nearly ready to go, Scootaloo tells her parents to come to the center of town, where many of the townsponies and others that the Crusaders have helped are holding a Crusaders Appreciation Day, to celebrate the importance of the trio. Skeedaddle points out how many ponies and other creatures the Crusaders have helped, and Mayor Mare gives them a special key to the town. As the event winds down, Snap and Mane wave Scootaloo over, and admit they never realized that her job with the Crusaders are just as important as their job, and they will allow Scootaloo to stay in Ponyville. Her aunts, already planning ahead, announce their plan to move to Ponyville and let Scootaloo live with them. Scootaloo runs to hug her parents and promises to visit them often, and then joins the celebration with Apple Bloom and Sweetie Belle.
- Adult Fear: Mane Allgood cites Sombra's return and the Tree of Harmony's destruction as the main deciding factors to keep the whole family together, implying that Scootaloo's parents are worried that something terrible could happen to Scootaloo if they aren't around to protect her.
- An Aesop:
- You have a job that can help others, but it might mean missing out on other things.
- Don't try to stop yourself from following your heart.
- Affectionate Nickname: Both of Scootaloo's aunts have one for her. Lofty calls Scootaloo "Slugger", while Snap calls her "Scoot".
- Anti-Villain: Scootaloo's parents are the force that need to be opposed in this episode by forcing Scootaloo to move away. However, they're not doing it out of any malice at all. It's because they want what's best for Scootaloo, genuinely love her, and are convinced to let her stay when they see just how much she means to everyone.
- Awesome Aussie: Snap Shutter speaks with an Australian accent, and his job has him frequently contend with all manner of dangerous creatures. His older sister, Aunt Holiday, also has a bit of an Aussie accent.
- Be Careful What You Wish For: Scootaloo is initially overjoyed at the idea of being with her parents all the time... until she learns it involves moving away from Ponyville.
- The Bus Came Back: Skeedaddle returns, having last been seen in "Marks and Recreation".
- Apple Bloom puts the potion-making skills she learned in "Twilight Time" to use, concocting one intended to keep the Crusaders from splitting up.
- King Sombra's return and the Tree of Harmony's destruction are brought up by Mane Allgood.
- Calling the Old Man Out: Scootaloo is not happy with her parents trying to dictate her life after having been gone so long. Scootaloo lets them know it after she resorts to chaining herself down to prevent them from taking her away.
- The Cameo: The Mane Six (minus Rainbow Dash), Spike, Starlight Glimmer and the Young Six make non-speaking appearances at the CMC appreciation day party.
- Canon Immigrant: Scootaloo's aunts Lofty and Holiday, who were introduced in the storybook "The Riddle of the Rusty Horseshoe", and then appeared in the Ponyville Mysteries comics, make their show debut in this episode (albeit with very different designs).
- Character Development: Snips is skeptical of the idea that Scootaloo's parents are explorers. He's come a long way from believing every boast Trixie made.
- Chekhov's Gun: Before the aunts leave for the weekend, Auntie Lofty is sewing a patchwork quilt but frets about having no idea for a theme. When Scootaloo runs away to their house, Lofty's found a theme — celebrating all the creatures that that Crusaders have helped — which inspires the subsequent celebration.
- Continuity Cavalcade: The crowd in the CMC celebration includes several characters they've helped over the show's run, including Babs Seed, Trouble Shoes, Diamond Tiara, Gabby, Feather Bangs, their campers from "Marks and Recreation", and Terramar.
- Continuity Nod:
- Cool Aunt: Aunt Holiday and Aunt Lofty.Aunt Holiday: [to Scootaloo] I left you plenty of healthy food for the weekend.
Auntie Lofty: And I left you cookies.
- Exact Words: The potion Apple Bloom brewed had the book description "On this potion, please depend. Any separation, mend. Friends together 'til the end." It ends up binding the Crusaders' hooves together.
- Fluffy the Terrible: The cragadile Snap and Mane brought with them is named "Marshmallow".
- Good Parents: Scootaloo's parents love her very much and want her to be as safe as possible, but also are entirely willing to let her stay in Ponyville when they see how much she means to everypony there. Their only real flaw is expecting her to want to move with them to Shire Lanka without even asking first.
- Innocently Insensitive: Scootaloo's parents, for expecting her to easily adjust to the idea of moving far away with only a few days warning. They've probably become so used to moving around and not having a permanent home that they've forgotten how important it can be.
- The Last Title: The second episode with this format after "The Last Roundup" back in Season 2.
- Literary Allusion Title: The episode alludes to Indiana Jones and the Last Crusade, mirroring how "Crusaders of the Lost Mark" alludes to the first film of the franchise.
- Never Smile at a Crocodile: A cragadile bursts into the schoolhouse and sends the students and Cheerilee into a panic before Snap Shutter jumps in and wrestles it to tie its mouth shut.
- No Celebrities Were Harmed:
- Scootaloo's father, Snap Shutter, is inspired by both Paul Hogan in Crocodile Dundee and the Crocodile Hunter Steve Irwin (his name and cutie mark are a nod to another of Steve's talents, photography).
- Her mother, Mane Allgood, references both Terri Irwin, Steve Irwin's wife, and chimpanzee-expert Jane Goodall.
- Ocular Gushers: Plenty of them between the Crusaders when Scootaloo's parents tell her that they're moving, especially at the last meeting.Apple Bloom: I hereby call the last meeting of the Cutie Mark Crusaders to order. First order of business... Cry! [they all start heavily crying]
- The Reveal:
- Members of Scootaloo's family are shown for the very first time in the show. In addition to her parents, her Aunts Holiday and Lofty appear (Holiday being Snap Shutter's older sister).
- We finally get to see Scootaloo's home for the first time beyond just her bedroom (which had been seen back in "Flight to the Finish").
- "Scooby-Doo" Hoax: The Crusaders attempt this in an attempt to trick Scootaloo's parents into staying, fabricating a fake creature costume, and passing it off as a new species.
- So Proud of You: At the very end of Cutie Mark Crusader Appreciation Day, Snap Shutter and Mane Allgood tell Scootaloo that, while they may have to miss their daughter growing up, they're very proud of her. And, if she wants to stay in Ponyville, she can stay.
- Status Quo Is God: Justified; Scootaloo ends up staying in Ponyville, but the episode does a good job of explaining why she should stay in Ponyville and how important a role she plays in helping everyone there as part of the Cutie Mark Crusaders.
- Tears of Joy: Scootaloo sheds these as she thanks her parents for deciding to let her stay in Ponyville. Her two aunts are seen getting misty-eyed as well.
- Wham Line: In the Cold Open, after the Aunts leave, Scootaloo receives a postcard and her reaction is unbridled excitement.Scootaloo: [Gasp!] They're coming home today!!
Sweetie Belle: Who?
Scootaloo: MY PARENTS!!!