"All In"
The episode begins with a flashback of Anne, Sasha, and Marcy pulling a prank on their school with a K-pop dance party, but they are all caught and sent to the principal's office. While Sasha and Marcy are let off the hook, Principal Murphy has a talk with Anne about letting her friends rope her into doing the prank. She asks Anne to write an essay about who she wants to be and what she wants to do with her life, then wishes her an early happy birthday.
In the present, Anne, Sasha, Sprig, Polly, Hop Pop, Grime, Olivia, Yunan, Frobo, Joe Sparrow, and Domino 2 are in restraints inside Andrias' castle while he is about to invade Earth. He then announces his invasion plans to the people of Los Angeles and unleashes his robot army, along with two giant mind-controlled herons. Anne and her friends all manage to escape with the help of Frobo and land safely in a swimming pool. Hop Pop recognizes the herons as the ones who killed Sprig and Polly's parents. Anne and her friends fight off the robots, but more arrive and surround them; they are rescued by Mr. X and Anne's parents, who are now FBI agents. They all regroup at the school, where Anne's parents supply some homemade Thai food and Polly upgrades Frobo with technology from the school's metal shop. Meanwhile, in the Core's hive mind, Marcy meets Andrias' father King Aldrich, who creates a fantasy world for her to enjoy so she can be assimilated into the Core.
Back at the school, Anne and Sasha come up with a plan: Anne, her parents, the Plantars, Domino 2, and Frobo will fight off the herons and the robot army while Sasha, Grime, Yunan, Olivia, and Joe Sparrow sneak into the castle to shut down its force field. Meanwhile at the castle, while Darcy is having fun destroying the city, Andrias remembers the day he first met Marcy and the moment he proposed his plan to stop her and her friends from fulfilling the prophecy to the Core. Back in the present, Anne and her team defeat more robots, but face trouble when the Plantars' trauma surfaces due to the herons. However, they manage to overcome their trauma, defeat the herons using the Plantar family hunting dance, and free them from Andrias' control, ordering them to destroy more robots. Meanwhile, Sasha and her team manage to infiltrate the castle and reach the force field generator. However, three Cloak-Bots attack, but Yunan and Olivia (who is given a laser blaster) fight them. Upon reaching the generator, Sasha and Grime are confronted by Darcy, and they begin to fight.
Back outside, Andrias arrives at the U.S. Bank Tower in a mech suit and gives an ultimatum to Anne; if she can beat him in combat, then he will call off the invasion, but if she cannot, he will destroy the city. Realizing who she wants to be, Anne accepts the challenge and flies on Domino 2 to begin the fight. She is initially overpowered, while Sasha and Grime try to fight off Darcy; Sasha ends up being hit by a dagger during the fight, and Grime tries to save her, which results in Darcy cutting off his arm. During Anne's fight with Andrias, she tells him that she feels sorry for him due to burying his feelings and closing himself off from others for almost a thousand years. As the fight rages on, Anne starts to become exhausted and is on the brink of defeat, but Mr. X and Anne's parents manage to empower Anne to continue the fight by playing her favorite song throughout the city. Both she and Sasha momentarily gain the upper hand, though the latter is injured by Darcy sneaking up on her and slashing her from behind. Meanwhile, in the Core's hive mind, Marcy begins to realize that none of what she sees is real, including her friends. She realizes that she forced Anne and Sasha to go to another world against their will, exclaims to Aldrich that she is done running away from reality and that she rejects both the Core and Aldrich who angrily leaves her to sit in pitch-black silence.
Anne continues to fight off Andrias but is continuously overpowered as her powers run out. Sprig then shows up on a heron with the piece of paper he found in his family's hidden tunnels, and with help from Mr. X's glasses, reveals that it is a message from Andrias' old friend Leif. Leif reveals through the message that after hiding the Calamity Box on Earth, she knew she couldn't go back to Newtopia, so she started a new life in Wartwood and founded the Plantar family. But, despite all the changes, she never forgot or stopped loving Andrias or all the good times she spent with him and Barrel. She also hopes that Andrias will not close himself off from others and that someday he will forgive her. After hearing this, Andrias breaks down in tears and now truly regrets all the horrible things he has done. Darcy tries to force Andrias to continue fighting, but Sasha defeats her by severing the neural link connecting to the Core's helmet, thus causing the Core to deactivate and freeing Marcy in the process. Andrias lets himself be defeated by Anne by blasting through his exo-armor, ending the battle and revealing that Andrias is a cyborg, which is how he was able to live for a thousand years.
With the force field down, everyone rushes toward Marcy, now unconscious, but she wakes up. She apologizes for her actions. Anne and Sasha forgive her, stating that wherever they are, they will always be friends, and everyone shares a group hug. However, the helmet of the Core reactivates and sneaks away. As Mr. X and Anne's parents clean up the damage with the help of the herons, Anne and her friends return to Amphibia, where the Resistance is still fighting and defeating Andrias' robot army. When the castle arrives, Olivia declares that Andrias and the Core have been defeated. However, just as everyone thinks it's over, Sprig notices the moon getting closer.
"The Hardest Thing"
Continuing where the last episode left off, everyone cheers for the victory of defeating Andrias, when the helmet of the Core blasts off into space, takes control of the moon, and drives it closer to Amphibia. When everyone notices it, Andrias reveals that the moon was where the Core's first pet projects were made and that the moon itself has been turned into a doomsday device meant to destroy Amphibia in case it is ever freed from the Core's control. Marcy realizes that the reason the Core is doing this is that it is afraid of being forgotten, so it is going to destroy Amphibia in a final desperate attempt to claim the stones of the Calamity Box for itself. Mother Olm then arrives, informing Anne, Sasha, and Marcy that the prophecy is near and that they must stop the Core. As everyone gets ready, Mother Olm tells Anne that while the stones themselves aren't strong enough to stop the Core, there is a hidden power that will work when someone has all the stones together. However, the cost of using it is the user's life.
When Anne arrives at the castle, Valeriana is there, ready to restore the power of the stones to Anne, Sasha, and Marcy. All three girls gain superpowers and colorful armor and fly up into space to stop the Core, but it fights back with an army of space robots. While the girls fight back, Aldrich, through the Core, tries to convince Andrias to help him. In response, Andrias finally stands up to his father and the Core, destroys his crown, and orders his robot army to help the girls stop the moon. However, despite their best efforts, Sasha and Marcy start to become weak, since they are not used to their powers like Anne is, so Anne decides to stop the Core alone by taking all three stones to use the hidden power within them. After a tearful hug and goodbye, Anne returns Sasha and Marcy back to Amphibia and prepares to face the Core.
When they get back, Sasha and Marcy tell the Plantars what Anne is going to do, and Sprig hops on Frobo to try and stop her. Anne and Sprig share a tearful goodbye and Sprig heads back. Anne then uses all the power from the stones to launch a huge blast of white light that destroys the moon, killing the Core in the process. However, she is petrified because of the combined power and falls down to Amphibia. She is then saved by Frobo, who takes her back to her friends, where she fades away in a stream of leaves, thus leaving everyone grief-stricken.
Suddenly, Anne wakes up in another world with a small house. She enters the house and meets an entity known as the Guardian, who takes the form of Anne's cat Domino, having saved Anne's soul and put it in a new body as a backup. The Guardian reveals that it created the stones 10,000 years ago and that Anne was the only one to use their power for good. It also offers that Anne takes its place as the new guardian, but Anne declines, saying that she still has her whole life ahead of her. The Guardian accepts this and resurrects Anne so she can live her life and probably become the new guardian after her life ends in 78 years. After her revival, Anne sees her friends still mourning her "death." After Sprig realizes that Anne is alive, the Plantars, Sasha, Grime, Marcy, and Frobo happily reunite with her and Anne then finds shards of the stones in her pocket.
Marcy states that the shards are a one-way trip home, so the trio bids farewell to their Amphibian friends. Marcy says goodbye to Olivia, Yunan, and Andrias, Sasha says goodbye to Grime, and Anne says goodbye to the Plantars and gives Sprig her cell phone. All three girls then head home with flower crowns on their heads, and when the portal closes, the shards and the Calamity Box turn to dust and disappear. With that, the frogs, toads, and newts all decide to rebuild their world together, with Polly getting a strand of hair.
Nine months later, Amphibia has now been restored to its original state, with everybody celebrating the defeat of the Core, and Andrias, now going blind and refusing his cybernetic enhancements, along with Barley, Blair, and Branson serving time for their crimes by helping to fix it. Everyone else is living happy lives, with Grime, Olivia, and Yunan as the toad and newt delegates for the new Amphibia government, Polly is now a fully grown frog, and Sprig is cataloging all the creatures in Amphibia using Anne's phone. As a statue of Anne is built within the center of Wartwood in her honor for saving Amphibia, Sprig goes on a journey with Ivy to unexplored territory that Grime discovered.
Ten years later on Earth, Andrias's attack, called "Frog-vasion", is questioned to be a hoax by the news. Sasha (who now works as a children's psychologist) and Marcy (who now works as a webcomic author) go to see Anne for her 23rd birthday. Anne now works as a herpetologist at the Aquarium of the Pacific, where she remodeled the amphibian section to look exactly like Amphibia, even naming a little pink frog Sprig. She then leaves to celebrate her birthday with her friends.
During the credits, a montage of important places in Amphibia is shown, with the final shot being a new group photo of Anne, Sasha, and Marcy.
