Twilight Velvet and Night Light, Twilight Sparkle's mother and father, are asleep when Twilight comes in and starts bouncing on their bed, excited for her first day of magic school. Her parents scold her for being up so early—Velvet noting it to be five in the morning. Velvet also makes it a point to mention that it's Shining Armor's first day of cadet school and "you don't see him leaping about!" A disappointed Twilight leaves, and her parents go back to sleep... only for Twilight to return moments later with Shining Armor, who bounces on the bed with her.
Twilight, Shining Armor, and their parents have breakfast at the breakfast table. Twilight and Shining's eyes meet, and they have a race to see who can finish eating first. Twilight wins and heads up the stairs, stating "the winner gets the bathroom first". Blushing, Shining Armor looks over to his parents, and Twilight Velvet comments on his immaturity.
As Twilight brushes her teeth, Shining Armor enters to show her his royal guard cadet uniform. As Twilight regards him, she sadly comments on how grown up he looks. Aware of his sister's concerns, Shining says he's not going away forever and that they'll see each other during his break in six weeks.
Twilight puts her toothbrush away and accidentally knocks over a bottle. The bottle falls on a tube of toothpaste, which squirts onto Shining Armor's uniform. Twilight's attempts to clean the stain only make it worse. Suddenly, she grabs the showerhead and showers her brother in water. Twilight chases Shining down the stairs with a hairdryer, and Shining pleads for her to stop helping.
Twilight Velvet thinks nothing of the spectacle and pours another cup of tea for Night Light.
Twilight waits eagerly for the taxi to arrive, but Twilight Velvet tells her staring out the window won't make it come any quicker. While they wait, Twilight tries on the saddlebag Velvet made for her. She races to her bedroom to pack some things in it, including Smarty Pants, and ends up packing so much that she walks lopsided. Twilight and her family come together for a photo. The weight of Twilight's saddlebag causes her to fall over just as the photo is taken.
The taxi arrives, and Shining Armor is nowhere to be seen. Twilight goes looking for him and finds him with Princess Cadance. The two of them say their goodbyes, Cadance giving Shining her mane ribbon and Shining promising to write her a letter every week. Twilight, excited to see her foal-sitter, comes between the two just before they kiss. Twilight teases Shining and Cadance over their puppy love, and Shining chases after her.
During the taxi ride, Twilight practices her magic with cat's cradle, Shining Armor remarking that she's getting really good. He takes the string from his sister and makes a figure shaped like her cutie mark. Impressed, Twilight attempts to recreate the figure but struggles with it. Her mother warns her not to force it, but it's too late: Twilight's frustration causes her to have a small magic surge that gives Shining Armor a flowerbed mane, her father large floppy ears, and her mother a mustache.
The taxi reaches a cliffside port where Shining Armor is to board an airship to cadet school. As Velvet fixes Shining's mane, Twilight looks at other cadets saying goodbye to their families and becomes sad. Shining comes up behind her and a messy mane. To cheer Twilight up, Shining pretends to be a swamp monster, and Twilight "vanquishes" him with a quill.
After the two embarrass themselves in front of several other ponies, a ranked royal guard officer approaches. The friendly officer asks Twilight if she wants to join the cadets too, as they "can always use somepony who can beat swamp monsters".
Twilight Velvet fixes Shining Armor's mane, and Shining, overcome with emotion, meets his parents for a hug. Twilight stands on a pair of suitcases so she can join in. As they embrace, a female unicorn cadet wheeling luggage to the airship bumps into Twilight's saddlebag. She gathers the luggage—and Twilight's saddlebag—onto the trolley and wheels them away. After the hug ends, Twilight realizes she no longer has any suitcases to stand on and hangs onto Shining Armor so she doesn't fall.
Shining Armor says goodbye to his family, giving them a salute, and boards the cadet school airship. Twilight notices her missing saddlebag and sees a unicorn mare loading it onto the airship. The distressed Twilight races to retrieve Smarty Pants and boards the ship before it casts off. She approaches the unicorn mare as she finishes talking with the ranked officer, and the cadet panics over there being a stowaway. The ranked officer returns to see what the commotion is about and watches as Twilight and the cadet panic in front of him.
As the cadet named Dizzy Star comes down her panic attack, the ranked officer, Sergeant Thunderhead, tells her to retrieve Twilight's saddlebag. As Dizzy Star walks away, Twilight asks Thunderhead about the scar on his right eye. Thunderhead tells of how, years ago, he was in the service of Princess Celestia and how his squad of royal guards was ambushed by a rogue griffon. Thunderhead had saved Celestia from the attack, and Celestia had saved Thunderhead from falling to his death.
Before Thunderhead can tell Twilight more, Dizzy Star enters alongside the squadron leader.
The squadron leader demands an explanation, and Twilight and Dizzy Star end up talking over each other. Shining Armor then enters, surprised to find his sister on the ship, and Twilight apologizes for the trouble she caused. Unfortunately, the airship has cast off, and Twilight is unable to get off: regulations prevent them from turning the ship around, Thunderhead has a crippled wing, and the port is too far away for Shining Armor to levitate her there with his magic.
Realizing the distress Twilight's in, Thunderhead offers to glide Twilight to the port. The two take off from the ship and glide toward the port. Thunderhead suddenly suffers pain in his wing, but with the help of the squadron leader's magic, they glide safely to the port. Unfortunately, Thunderhead's act of kindness leaves him unable to return to the ship.
Back in the taxi, Twilight waves goodbye to Thunderhead as a pair of Pegasi lift him to the airship. Twilight suddenly starts to miss Shining Armor and asks Smarty Pants what they're going to do now.
Twilight looks at a clock tower and asks the two cabbie ponies how long it'll take to reach the school. One of the cabbies says twenty minutes, and Twilight worries she'll be late. One cabbie suggests taking a shortcut. The other cabbie refuses at first, but he agrees when he sees how sad Twilight is. Unfortunately, the shortcut causes the taxi to get stuck in a patch of mud.
Princess Celestia and her aide Raven greet new students in front of the school. Princess Celestia becomes briefly saddened over what happened with Sunset Shimmer; as Twilight and her parents arrive, Celestia assures Raven that "it won't be the same this time". Celestia notices the three are covered in mud and forgives them for being late; she doesn't even get the least bit upset when Twilight accidentally gets mud on her face.
Twilight says goodbye to her parents and goes with Celestia into the school. After they wave goodbye to their daughter, Twilight Velvet holds Night Light close as she cries with pride.
Twilight and Princess Celestia enter the school, Twilight remarking how big it is. Celestia sees one of the school's instructor trip down a flight of stairs. As she goes to help him up, Twilight says hello to a pair of unicorn fillies, Orange Twist and Lemon Burst, who are immediately put off by Twilight's coat of mud. Orange and Lemon proceed to tease and intimidate Twilight about how the school works, but Princess Celestia catches them and demands they report to her office at 3 o'clock.
In Celestia's quarters, she and Twilight wash up, and Celestia gets briefly emotional when she sees Smarty Pants. Suddenly, the infant dragon Spike starts crying. He only stops crying when he comes face-to-face with Twilight. Celestia tells Twilight that Spike constantly cries with hunger but never eats more than a few spoonfuls of whatever he's fed.
Twilight gets the idea of feeding him a ground-up mixture of gems and the eggshell he was hatched from. Celestia and Raven are beyond impressed that Twilight's gotten Spike to eat, and Twilight admits she got the idea from a storybook. As Twilight burps the fed Spike, he spits up on her.
On their way to Twilight's first class, Twilight and Celestia bump into P.E. instructor Willow Wisp. Twilight admits to not being the athletic type, but Willow assures her they'll find something she'll enjoy.
The two pass by a painting of Star Swirl the Bearded. Celestia excuses herself to smooth things over with the school dean Gisela. During her time alone, Twilight fantasizes about being Star Swirl the Bearded, making a beard out of a mop head. She accidentally fires off a beam of magic as Celestia returns with Gisela. The beam hits Gisela, giving her a beard, and she scolds Twilight for using magic in the hallways.
Princess Celestia removes Gisela's beard with her magic. Gisela escorts Twilight to where she was giving her speech, and Princess Celestia sees the little filly off with a wink. Celestia walks through the school hallways and passes by some friendly faces, including Inkwell, before returning to her quarters. After relieving Raven of her dragon-sitting duties, Celestia removes her royal regalia and collapses onto her bed in laughter.
Twilight and Gisela enter homeroom, and Gisela tells Twilight to take her seat. As Gisela continues her student orientation lecture, Twilight asks a unicorn filly sitting next to her if she can copy her notes to catch up, to which the filly happily obliges. Twilight is so vigorous in her note-taking that she accidentally splashes some quill ink on the filly next to her.
As Gisela moves on to the students' timetables, she finds a packet of stickers in her saddlebag; attached to it is a note from Shining Armor reminding Twilight to "never forget to keep having fun". Twilight uses the stickers to map out her schedule, but the feathery end of the quill in her mouth tickles her nose. She sneezes, and the filly next to her becomes covered in stickers. Gisela sees the sight from the front of the classroom and tells Twilight "arts and craft clubs are after school".
As Gisela concludes her lecture, the school bell rings, and Gisela sends the students off to their first class. As she struggles with her heavy textbooks, Twilight asks Gisela if they're expected to carry them around all day. Gisela tells her that if she wasn't late for orientation, she'd already have her locker key. She also tells Twilight that she'll have to learn to be more organized if she wants to succeed at the school.
Twilight goes to put her books in her locker—#19—but struggles with the lock. She remembers how Shining Armor used to unlock the cupboard at home with magic, so she tries to open her locker like that. Unfortunately, this triggers the locker's charm-safe protection magic, and Twilight is blown back into the lockers behind her. As she collapses on the hallway floor, Twilight is mortified to discover she read her locker key number upside-down; her locker number isn't 19, but 61.
Twilight leaves Smarty Pants in her locker and looks at her schedule, reading that her first class is Equestrian Literature with instructor Miss Flyleaf. As she races upstairs so she isn't late for another class, she finds a Pegasus teacher leading a group of foals. The teacher, Miss Flyleaf herself, notices Twilight and is relieved to have not lost one of her students on her first day of teaching.
A confused Twilight asks where the class is going, and Miss Flyleaf says they're going to the library. Twilight becomes starry-eyed at the thought of how big the school library is, and Miss Flyleaf talks up the library's wonders. As an awestruck Twilight runs ahead in the library's direction, Miss Flyleaf sighs over having lost a student again.
Twilight bounces to the library ahead of her teacher and classmates, gasping and tearing up at its magnificence. When Miss Flyleaf and the other students catch up, Flyleaf scolds Twilight for running off. The students line up to take pictures for their library cards, and Twilight is still in awe of the library. Unfortunately, her over-excitement causes Flyleaf and librarians to shush her several times.
Just as Twilight's picture is taken, she races to see the giant library hourglass turn over, causing her photo to be a blue and purple blur.
Miss Flyleaf sends her students off to pick out two books; as soon as Twilight is given the say-so, she gallops off in excitement. Just before she takes Daring Do and the Trek to the Terrifying Tower off the shelf, a much older stallion takes it first and walks into a nearby room. Twilight follows him inside and finds what appears to be book-torturing devices.
When Twilight wails at the stallion for "torturing books", he laughs and explains that he's only rebinding them. He says books are precious things that need to be treated with respect—a sentiment that Twilight heartily agrees with. When Twilight says she wanted Daring Do and the Trek to the Terrifying Tower, the bookbinder tells her to start at the series' beginning and gives her a freshly-rebound copy of Daring Do and the Quest for the Sapphire Stone.
As Twilight trots off happily with her book, she scolds another student for mistreating one of her books as the bookbinder watches.
Miss Flyleaf gathers her students together to return to class, and Twilight says she needs to use the restroom. After giving Twilight directions, Miss Flyleaf goes after the other foals.
In the restroom, Twilight overhears a conversation between two older mares. As she washes her hooves in the sink, the two mares spray too much perfume on themselves, and Twilight quickly opens a window. She knocks into her saddlebags, causing her books and scrolls to fall in the sink water. She uses the nearby hoof dryer to dry them off, but the lesson bell rings.
Not wanting to late for class yet again, Twilight uses magic on the hoof dryer to dry her damp books and scrolls faster. The dryer expels so much air that Twilight is hurled out the window. Miss Flyleaf sees Twilight outside and rescues her from a tree.
After Miss Flyleaf sees her off safely, Twilight heads to her next class—science—but she fears what might happen in that class after the day she's had. As she nervously enters the science lab, Twilight is unnerved by some of her would-be classmates, but she is pleased to meet a fellow book lover: a shy filly named Moondancer.
As the instructor introduces her students to the wonders of science, Moondancer accidentally knocks a book off her desk. When it thuds on the ground, the jumpy Twilight ducks for cover.
Overall reception for Twilight's First Day has been largely positive, with many praising its art style, story, and generally cute appeal. The comic is consistently featured in comic spotlights on Equestria Daily, Discord's Domain, and FOB Equestria.
The first comic has become the artist's most viewed submission on deviantART and even reached #4 on deviantART's "Most popular in the last 24 hours" listing.