In the Pride Lands of Africa, a lion rules over the animals as king. The birth of prince Simba son to King Mufasa and Queen Sarabi creates envy and resentment in Mufasa's younger brother, Scar, who knows his nephew now replaces him as heir to the throne. After Simba and his cousin Lyre have grown into young cubs, Mufasa gives them a tour of the domain, teaching them the responsibilities of being rulers and the circle of life. Accompanying Mufasa is a feral teenager named Lita, who has lost her memories and has been since adopted by the king to raise her on the right path. Later that day, Scar tricks them and their best friend Nala into exploring a forbidden elephant graveyard, despite the protests of Mufasa's hornbill majordomo Zazu. At the graveyard, the spotted hyenas Shenzi, Banzai and Ed attack them before Mufasa and Lita, alerted by Zazu, rescue them, with Mufasa forgiving Simba for his actions. That night, the hyenas, who are allied with Scar, plot with him to kill Mufasa and Simba.
The next day Scar lures Simba to a gorge and tells them to wait there while he gets Mufasa. On Scar's orders, the hyenas stampede a large herd of wildebeest into the gorge. Mufasa rescues him, but as Mufasa tries to climb up the gorge's walls, Scar throws him back into the stampede, where he is trampled to death. After Simba finds Mufasa's body, Scar convinces him that his is responsible for his father's death and advises Simba to flee the kingdom. As Simba leaves, Scar orders the hyenas to kill the cub, but Simba escapes. Scar announces to the other lions that both Mufasa and Simba were killed in the stampede ands steps forward as the new king, allowing a pack of hyenas to live in the Pride Lands. His first order as king is to have Lita become his guardian and have her prevent any Sailor Scouts from entering the kingdom.
Meanwhile, the Sailor Scouts, while traveling on the Lunar Crescent ship, receive a distress signal from Rafiki by way of magic vision on Rei's part. Serena immediately turns the ship towards the Pride Lands, but Rei is more cautious, believing the vision could lead to a trap. Although Ami tries to break up the argument, Serena ends up crashing the ship in the middle of an oasis, separating the Sailor Scouts from Rini in the process.
After running far away, Simba collapses from exhaustion in a desert. Timon and Pumbaa, a meerkat and a warthog, find him and nurses him back to health. Simba subsequently grows up with them in the jungle, living a carefree life with their friends under the motto "hakuna matata" ("no worries").
Meanwhile, Rini ended up in another part of the jungle all by herself, where she begins to feel lonely and scared without her friends. She hopes that her mother can find her soon because she feels cold, most likely due to Scar's continued prescence in the Pride Lands. Meanwhile again, Serena and Rei are still mad at each for crash-landing the ship in the middle of a kami-forsaken jungle with no help in sight other than "a stupid monkey" as Rei puts it. Ami still tries to make them apologize to each other, but she soon realizes that Rini is missing and that the two better get their act together in order to find the poor girl. Thankfully, they are approached by a group of ponies named the Mane Squad. Led by Twilight Sparkle, they reveal that they too received a distress signal from this world, and that they will help aide the Sailors in saving the Pride Lands by any means necessary. Back at the Pride Lands, while Scar had a little chat with the hyenas about the state of affairs in the kingdom, Lyre and Lita decide that enough is enough with Scar's rule and that they need a true king to set everything right, getting Nala in on their plan for escaping the wasteland. Pauly the parrot, an old friend of Zazu's, warns them to escape quickly, otherwise they might get spotted, to which they avoid successfully upon their release.
Later the next day at the oasis, a now adult Simba rescues Timon and Pumbaa from a hungry lioness, who turns out to be Nala. During the confusion, the three Sailor Scouts and the Mane Squad end up finding Rini hiding behind an old tree, relieving Usagi of her distress and getting her to apologize to Rei for her reckless abandon earlier. But no sooner does Rei apologize in turn when she suddenly gets a brief vision of Mufasa falling to his doom, and Scar in silent conversation with a very familiar evil faerie. Rei doesn't understand what this means yet, but she is interrupted in her thoughts by an introduction to Nala, Lyre, and Lita all at once. Luna the cat senses something very familiar about Lita, and advises the Sailors and Ponies to keep an extra-close watch on this "feral" girl.
While the heroes leave Simba and Nala alone, the two lions fall in love with each other after reconciling. Nala and Lyre urge Simba to return home, telling him the Pride Lands have become a wasteland with not enough food and water. Feeling guilty over his father's death, Simba refuses and storms off, leaving Nala and Lyre disappointed and angry. As Simba enters the jungle, he encounters Mufasa's mandrill friend and advisor, Rafiki. Rafiki tells Simba that Mufasa is "alive" and takes him to a pond. There Simba is visited by the ghost of Mufasa in the sky, who tells him he must take his rightful place as the king of the Pride Lands. Simba realizes he can no longer run from his past and goes home. Nala, Timon, Pumbaa and the others join him, and agree to help him fight.
At the Pride Lands, Simba confronts Scar, who taunts Simba over his "part" in Mufasa's death. But when Scar pushes Simba to the edge of Pride Rock, he admits he himself killed Mufasa. Enraged, Simba roars back up and forces Scar to reveal the truth to the others. Upon Scar's forced revelations, he then goes on to reveal that he was in fact working for the evil faerie Maleficent all the time, and that he is but the first of many members of a secret alliance known as the Hellfire Organization, who, he claims, will ravage all worlds until the universe belongs to them alone and the "door" finally opens. It's at this point when Luna finally realizes what Rei's vision was all about, and gives the signal for the heroes to stop Scar before he destroys this world.
At once, the transformed Sailor Scouts, the Elements of Harmony, Lita, Lyre, Timon, Pumbaa, Rafiki, Zazu, and the lionesses fend off the hyenas while Scar, attempting to escape, is cornered by Simba at the top of Pride Rock. Scar begs Simba for mercy, saying he is family and placing the blame on the hyenas. Simba says he does not believe Scar anymore, but spares his life and commands him to forever leave the Pride Lands. Scar meekly walks past him, but then attacks his nephew, transforming into a ferocious monster called the Groundshaker thanks to the powers of darkness he gained from Maleficent. Lita charges up the mountain to help save Simba's butt from his uncle even though he's way out of her league due to having the power level of Chuck Norris. But as she continues to fight even after getting beaten down repeatedly by being kicked in the groin, the mark of Jupiter appears on her forehead, causing Luna to remember that Lita is Sailor Jupiter, and throws at her the Green Transformation Pen, urging her to use it to become Sailor Jupiter at once to stop Groundshaker Scar and help save Simba. She does so, and with a flash of lightning, Sailor Jupiter comes thundering in, with all her memories restored in the process.
After a fierce battle, Sailor Jupiter uses a Thundering Clash to destroy the Groundshaker shell, exposing Scar as he falls. But he's done yet as he uses his fall to try one last attempt at killing Simba, only to fail as Simba uses a throwing flip to send his uncle careening off the cliff to his supposed doom. Scar survives the fall, but is attacked and killed by the hyenas, who overheard his attempt to betray them. With Scar and the hyenas gone, Simba ascends to the top of Pride Rock and takes over the kingdom as the rain falls again. Sometime later, with Pride Rock restored to its former glory, Simba looks down happily at his kingdom with Nala, Timon, Pumbaa, and Lyre by his side; Rafiki presents Simba and Nala's newborn cub to the inhabitants of the Pride Lands as the "circle of life" continues.
The next day, Serena gushes over Lita's return and how she has become a beautiful seifuku maiden instead of a ragged feral girl. Lita takes offense at this comment, but the other Scouts calm her down with an offer to rejoin their team and save the worlds from this "Hellfire Organization" that Scar mentioned earlier. She agrees, but only if Lyre comes with them because she is her friend after all. They accept, and so they ride off to a new adventure.
- This films takes place after Timon and Pumbaa's Adventures of Sailor Moon in which Sailor Moon and her friends already knowing Timon and Pumbaa.