The Return of Queen Chrysalis is the first arc of the comic series by Katie Cook. It is set between Seasons 2 and 3, and features the return of season two antagonist, Queen Chrysalis.
Issue #1 was released on November 28th, 2012. Issue #2 was delayed and released on January 1st, 2013, causing Issues #3 and #4 to be delayed as well. Issue #3 was released on February 6th, 2013. Issue #4 was released on March 6th 2013.
The next day, Applejack, Rarity, and Rainbow Dash notice that the Cutie Mark Crusaders are acting weird, as are all the ponies in Ponyville . Twilight Sparkle realizes that they are the changelings, who have returned and are now after Ponyville. She has Spike send a letter to Princess Celestia, but receives a letter in response saying she is unavailable due to a royal emergency.
Taking the matter into their own hooves, Twilight Sparkle, Rainbow Dash, Rarity, Fluttershy, Applejack, and Pinkie Pie go out to rescue the ponies of Ponyville. They find Derpy imprisoned in a cocoon while a changeling takes her form. Another changeling hits it on the head to make it cross-eyed. After the two changelings fly away, the ponies enter a building with an eerie green glow. Here, they find the ponies imprisoned in cocoons by changelings. The group defeats the changelings, with Pinkie Pie trapping the surviving changelings with a bubblegum cannon. They rescue all the ponies except the Cutie Mark Crusaders, who remain missing.
Through Spike, Queen Chrysalis sends the group a crystal ball in which she can communicate with them and shows them the Cutie Mark Crusaders imprisoned in her kingdom. Queen Chrysalis then tells them to come to the rescue of the Cutie Mark Crusaders in three days, or else she'll do "something bad" to them. She cuts off the transmission when Scootaloo comments that she is monologuing and is about to reveal her plan. The crystal ball becomes a map to the changeling kingdom.
Twilight says that in three days the Secretariat Comet will pass over Equestria, saying it is the biggest conjunction in celestial events in over three thousand years, and every magical creature will feel its effects. Twilight suspects that Princess Celestia is occupied with protecting Canterlot. Although they suspect a trap, the group sets off towards the changeling kingdom, leaving Spike in charge of the captured changelings and getting a hold of Celestia to resolve the issue.
Issue 2 begins with the ponies in the Macintosh Hills. Twilight discusses the route they'll take to get to the Changeling Kingdom, and mentions that the fastest way is through the mountain. Rainbow Dash retorts that the fastest way for her is flying over the mountain, but Applejack insists that the main six stay together as a group.
The six find and enter the cave, where they run into a cave troll, and Twilight asserts that it's much larger than the "Cave Dweller's Reference Guide" says that species is. The troll picks up Fluttershy, and brushes her mane with a branch, eventually setting her down on a shelf containing what looks like a giant stone Magic 8-Ball and Optimus Prime. He grabs Rainbow Dash next, dolling her up, much to Applejack's amusement and Rainbow's annoyance. Rarity then comes up with an idea, and asks Pinkie for help. The idea turns out to be rock and wood replicas of the main six. The troll grabs the Rarity doll and states that he will call it George, much to her horror. Twilight then pulls out the gem to check on the map.
The comic then cuts to Queen Chrysalis, and she states that trolls are the most idiotic creatures. She then overhears the Cutie Mark Crusaders rambling on about getting cutie marks in toy making or troll hunting, and comments that trolls might be the second most idiotic creatures. She then sends her changeling minions out to enact a plan.
Back in the caves, the changelings cause a cave in, separating the ponies into three groups: Applejack and Rarity, Pinkie Pie and Rainbow Dash, and Twilight Sparkle and Fluttershy. The changelings transform into the main six.
Pinkie Pie and Rainbow Dash think they see Applejack and Rarity, and Rainbow, carrying Pinkie, flies down, only to overhear Applejack stating that she thinks Rainbow Dash is full of herself, and Rarity saying that she thinks Pinkie Pie is the most annoying pony she'd ever met. This angers Rainbow Dash while saddening Pinkie Pie, making her hair deflate. In another part of the caves, Twilight and Fluttershy overhear Rainbow Dash stating that she thinks Twilight is a know-it-all egghead, and Pinkie Pie stating that Fluttershy was useless to bring along, being scared of her own shadow. The reactions are shock for Twilight and sadness for Fluttershy. Finally, in another part of the cave, Applejack and Rarity overhear Twilight and Fluttershy, with Twilight mocking Applejack for thinking she's in charge, without having Twilight's knowledge or magic, and Fluttershy stating that she can't believe Rarity came along, as she felt that keeping her hooves clean would matter more than her sister. In this case, both Applejack and Rarity are angered, and Applejack suggests that they go and get their sisters without the help of the others.
When the groups eventually reach the end of their path, they begin to loudly (verbally) fight, until Twilight notices a giant spider looming over them. All the main six are terrified by the gang of giant spiders, except for Fluttershy, who is fascinated, and speculates that he is probably a big sweetie, just like the troll. However, upon looking into the spider's eyes, Fluttershy realizes the spider's less-than-friendly intentions. One by one, the ponies, except for Twilight and Pinkie Pie, are captured in webbing. Pinkie runs off, stating she has an idea, leaving Twilight to try and deal with the spider with her magic, though that fails. Just then, Pinkie returns with the cave troll, whom she has convinced of there being a teddy bear where the other ponies are. The troll, named Jim, sees the spider and is convinced that's the teddy bear, so he drags the spider off, naming him Fluffy.
Later, after the ponies have been unstuck, the ponies resume their bickering, much to Queen Chrysalis's amusement. The Cutie Mark Crusaders then comment on sports they think are more fun than watching six friends become enemies, much to Chrysalis's annoyance.
Eventually, the ponies split up into their groups of two again, and go their separate ways. Rainbow Dash worries that they're lost without the map now, but Pinkie asserts that she knows where they are. When Dash questions her, she asserts that they're in the woods.
The third issue begins with a flashback to Chrysalis's first defeat, sent flying into the distance. She and some of her changelings land in the center of a town inhabited by catlike people with lots of love. Although she survives the fall, she and her army are weakened, so they feed off the cats' love and transform their town into the Changeling Kingdom. Still too weak to invade Canterlot, Chrysalis decides to absorb Twilight Sparkle's magic when the Secretariat Comet eventually flies by. The comic then returns to the present, where the Cutie Mark Crusaders continue to annoy Chrysalis with their banter. Chrysalis then checks in on Twilight Sparkle, who is having a conversation with Fluttershy, in which Fluttershy convinces Twilight to forgive the other ponies. Twilight then checks the map, and observes that they'll meet up outside the gets of the Changeling Kingdom, providing none of them turned around and went home.
Next, a changeling minion delivers a report on how Applejack and Rarity are doing, causing Chrysalis to burst into laughter over their clashing personalities. Finally, a report is delivered on Pinkie Pie and Rainbow Dash: Pinkie has costumes for her and Rainbow Dash, as well as for the changelings to wear. These costumes consist of giant likenesses of the pony/changeling to wear them. Chrysalis remarks that if she hadn't been watching Pinkie for hours, she wouldn't believe her minion's report. Additionally, in that report, Rainbow Dash begins to see through the changelings' deception, causing the Cutie Mark Crusaders to cheer out at the thought of the Mane Six becoming friends. Chrysalis then retorts that she doesn't care if they're friends or not, it was just an entertaining bonus to see them squabble. She reveals that her true plan is to destroy Twilight, then when her friend's emotions peak, to have her colony feast on them. After that, she states her intention of returning to Canterlot and watching Equestria crumble. She presumably kills one of the cats in front of the CMC.
The comic then returns to Twilight and Fluttershy, where Twilight remarks that the map is very accurate, even pointing out a hole, which the two promptly fall into. Twilight is able to use her magic to get the both of them out of the hole, and once they're out, they spot a Chupacabra. Twilight observes that they only eat goats, but then she and Fluttershy realize the twigs lodged in their manes look like goat horns, and so the Chupacabra begins to chase them.
Rarity and Applejack are walking amongst flowers, with Rarity enjoying the scenery, but Applejack discomforted by the feel of the area. Rarity attempts to pluck a flower to take home in order to work into her clothing, but stops when Applejack alerts her to what she thinks are snakes, rustling in the bushes. They soon discover that it is not snakes; rather, it is the flowers themselves: Pony Eating Petunias, as Rarity calls them. The two ponies jump into the water, and onto a log, where two of the flowers follow. Applejack attempts to get them to fall off by spinning the log, but before that can happen, the group reaches a waterfall. The ponies grab onto the bases of the flowers, in order to use the flowers as parachutes.
Pinkie Pie and Rainbow Dash happen upon a group of rabbits with horns. One bites into Pinkie's left hind leg, freaking Rainbow Dash out, but only causing Pinkie to give that one the name "bitey". Rainbow Dash picks up Pinkie by the tail and starts to fly out of there, when Rarity and Applejack crash into the two. Applejack uses one of the flowers to take out some of the bunnies, and the group continues to run again. The flowers do not seem to partake in the chase. They then bump into Twilight and Fluttershy, causing the whole group to tumble down a cliff. Twilight hopes that such a death-defying fall might keep their pursuers at bay. It is at this point that Fluttershy reveals the bunnies' species to be Vampiric Jackalope, as she mentions that they are natural enemies of the Chupacabra, and will fight with it for dominance, and the right to eat the ponies. They then engage in a fight which disgusts/horrifies the ponies, with the exception of Fluttershy, who only remarks that nature is fascinating.
The group exchanges apologies, and Pinkie brings out an "I'm sorry" cake she had been carrying, in addition to putting her costume back on. She convinces the group to eat the cake, while the issue cuts to Chrysalis one final time. Spike then narrates the ending to the issue, and sets up the stage for the next one, which he states will be contain the conclusion.
As the Mane 6 reach the changeling kingdom, they talk of a plan for defeating Queen Chrysalis and rescuing the Cutie Mark Crusaders. Inside, the Cutie Mark Crusaders say Twilight will beat Chrysalis, and Chrysalis realizes she doesn't need the Cutie Mark Crusaders anymore, intending to kill them rather than let them go.
The Mane 6 enter Chrysalis's castle, which is a labyrinth of stairs and doors, where Chrysalis tells them to find her behind one door, but the others have surprises. As they each open a door, Pinkie Pie finds a giant eyeball, Applejack finds Mola Ram with an apple in his hand saying "Kalima!", Fluttershy finds Pennywise saying "Hey Georgie!", Rainbow Dash finds the twins from The Shining (which she says is boring), and Rarity finds the Phantom of the Opera. Twilight finds the right door, which asks a riddle "How is a pegasus like a writing desk? Can you answer this riddle?" As the others think of the answer, Pinkie Pie says "Nope! I can't answer it!" The door says she is correct, and opens.
The Mane 6 confront Chrysalis. While Twilight fights her, her changelings imprison the other five in cocoons. Twilight shoots a powerful blast of magic which does little to Chrysalis but destroys part of the wall, and Chrysalis decides that instead of draining Twilight (to which Twilight says she wouldn't be able to use her magic because she learned it by studying), she will make her her apprentice. Twilight initially refuses, but when Chrysalis threatens to drain her friends if she doesn't, and says she won't if she does, Twilight accepts. Chrysalis reveals her intent to drain Twilight's love and have her drain her friends instead. When the Secretariat Comet flies by, Twilight beats up Chrysalis with her magic, eventually defeating her and her changelings with a powerful magic beam.
Some time after, Princess Celestia arrives with Spike. They were fighting an army of giant cockatrices in Canterlot when the comet flew by. Spike helped defeat them with a trident. They also had to deal with a giant marshmallow pony in Manehattan (a reference to Gozer's final form in Ghostbusters). They tell each other the stories of their adventures. As for Chrysalis, she and her changelings are imprisoned in their castle by Pinkie Pie, who annoys them with her costume at the door asking riddles and singing the song that never ends, while Twilight says she won't be able to break out for a while.
At the end, the battle where Celestia and Spike fight the cockatrices is shown, with Spike telling Celestia everything as they are in the middle of the battle.