In 1588, two children are walking along the beach when they see a couple of bodies laying on it, dead. Off the coast, they see a naval battle raging. It is the Spanish Armada, and they have been defeated in their attempt to invade England. When King Philip II of Spain receives the news, he decides to do the forbidden: use the Ministry's doors to go back in time and ensure the Armada is victorious. However, the Secretary of the Ministry will not reveal which doors to use, not even under torture.
Meanwhile, Alonso (who woke up that morning to find Elena has left, needing some time to understand what Alonso told her in the previous episode), Amelia and Julián are sent to 1809, with the task of saving Agustín de Argüelles, one of the first Spanish constitution's fathers, who has joined the resistance in Asturias instead of going to Seville. The trio saves him and most of his companions in the nick of time, and escort the man to Seville.
In the meantime, the alert has gone out from the 1588 Ministry, and Salvador sends another patrol to investigate. Unfortunately, this guides the King to the 2016 Ministry, which he takes over (second time this happens) with a large group of soldiers, and tries to learn what went wrong with the Armada to change things. Salvador tries to prevent him from changing history, but the King murders him and decides that, for the good of Spain, he will use the Ministry to meddle with history and preserve the Empire. Then, the same two children from the beginning walk along the same beach, but this time the battle has changed: the Spaniards are victorious.
Just then, the trio comes back and notices everything has changed around them: everyone but them wears a suit, there are strange posters hanging everywhere... and when they go to report the events of their mission, it is Ernesto who welcomes them, telling them he is glad they got rid of Argüelles, cold-heartedly chuckling about the man's attempts to make Spain a democracy. Amelia stops the others before they can say anything, having seen a photograph of Ernesto shaking hands with King Philip II, and then comes Irene... a very much changed Irene: black hair, submissive, and asking for free time to spend it with her family. Before the trio leaves, Ernesto tells Amelia she can return to Administration and gives Alonso a present: a set of baby clothes. Both Alonso and Julián go back to their homes, while Amelia researches.
While Alonso discovers he is married to Elena and she is expecting and Julián meets with Maite, Amelia finds out that history remains unchanged from what she remembers until the Armada's victory in 1588, upon which time Philip II openly revealed the existence of the Ministry and became King of Time, ruling over all of the Empire in every point in time after 1588, having anyone that could be considered dangerous killed to ensure no one can disturb his empire. When Amelia meets with the others and tells them she has a plan to restore history as it should be, both men have doubts: after all, this is a world where they are with the women they love, and Alonso is pretty much living in a world where many things he had wished to see are real. Amelia tells them that, no matter what they do, she will do her own part.
Amelia gets to meet Irene alone on Ernesto's office, where they talk while they have a drink, and Amelia decides the one way she can get Irene on her side is by calling back to their first meeting: kissing her. While passionate at the beginning, soon Irene steps back, horrified with herself: obviously, not even the Inquisition can suppress Irene's lesbianism. Irene fears Amelia is a trap sent by the Inquisition, but Amelia soothes her, telling her of the world that should be, one where Irene is free to love whoever she wants, and where she is a high-ranked officer in the Ministry, instead of a secretary. Irene promises to keep Amelia's secret if she will keep hers.
That night, Julián and Maite go to Alonso and Elena's house for dinner... and Julián is already starting to think that this world is not right. The Maite he fell in love with was an independent, strong woman who would probably throw a dish to his head if he did not help with the housework: instead, this Maite is submissive, accepting the "traditional" role of a woman. And Alonso knows, too, that this is not the Elena she loves, behaving more like Blanca, the wife he had to leave behind in the 16th century, but tries to hold onto the idea. Before dinner, though, there is a Saber y Triunfar program (presented by Jordi Hurtado, his second cameo in the series), and a speech from King Philip II where the man reveals that the war with the United States and the muslims continues, that unemployment has gone down to 2% and asking people not to forget to pay their taxes. When the two women monotonously pray a modified Credo that praises Philip II almost like a god, the two men start to see things have changed too much.
The next morning, Amelia begins her part of the plan, knowing it is bound to be a Suicide Mission if Alonso and Julián don't help: she goes to 1588 and starts to play the role of a prophet, stating that the king should not be all-powerful, and that people have rights... while she looks at a CCTV camera hanging from a nearby building. Soon, she is arrested and taken before the King, to whom she reveals she remembers history as it should be and that she knows how he will die. The King orders her to be tortured by the Inquisition (which she is, with an electric chair) and calls 2016 so Ernesto will arrest Alonso and Julián.
While the two men discuss this present, and Julián says that they should help Amelia - in his own words, Maite and Elena "have the same body, the same voice, but not the same soul" - they receive a call to go to one of the gates. Irene is there, and tells them both that Amelia has been captured and that they are to be arrested, before asking them if what Amelia told her was true. Both of them confirm it. Irene decides to help them with Amelia's plan.
Soon, Ernesto calls to the King, telling him that they have just captured Julián, and he starts to beat the crap out of him. Both Amelia and Julián are being asked about who is behind whatever plot is trying to restore history, and Amelia is probably on the edge of death, when the King receives a photograph: one of himself, sleeping, at age seven. While Ernesto and the King were distracted, Alonso went back further in time to find young Philip in a vulnerable position, and now tells the King he can choose: let Amelia and Julián go and do what Amelia tells him to do, or die well before he can be king, unknown by anyone. Shaken, the King follows, and Amelia tells him to stop himself from trying to change history, promising to do something about his future undignified death.
Back to the same beach, and the same children, and once more Spain has lost. This time, though, the King cries for everything lost because of him. In the present Ministry, Salvador greets the trio back, congratulating them for carrying out their mission to save Argüelles. Ernesto is back to the friendly man he has always been, and Irene has recovered her blond hair and sunny disposition. Only the trio remembers the events of the changed timeline. Alonso returns home to find Elena has come back: the strong, independent Elena has apparently decided she did not believe him when he said he traveled in time. Julián goes back to his favourite bar, but he is alone: Maite, obviously, is still dead.
The last scene is of Philip II, alone in his bed: it is clear he is on the edge of death. But he soon has a visitor: Amelia, disguised as a nun, ready to make good on her promise. The King reveals that he is afraid of death, but Amelia (tearing up) gets him to think of a happy memory: his mother visiting him in bed, kissing him in the brow, and telling him he will become a great king, like his father. Philip breathes his last, and Amelia closes his eyes before leaving the room.
End credits.
