It is 1828. Bogotá. Alonso and Pacino are in front of an execution squad, but before they open fire, a man on a horse stops them: Simón Bolívar (who already crossed paths with them), who wants to interrogate them.
In the present, Marta is still in coma, and unlikely to get better. Salvador, Irene and Ernesto discuss the current situation, when Angustias comes in: a group of men, women and children wearing ancient clothes are guided by a man with a torch through a tunnel with modern lights, much to their surprise, a feeling increased when they arrive to modern day Madrid: they are Moriscos
, escaping from 1609. The Ministry becomes suddenly overstretched by an unexpected crisis of enormous proportions. Ernesto and Lola go to meet the refugees, while Irene remains back.
In 1828, Alonso and Pacino meet with Bolívar, and present him with documents to put an end to the war between Spain and the American colonies, with the former recognizing the latter's independence. Bolívar appears to remember them, but the two deflect his suspicions by giving them false names. While Alonso and Pacino retire, Bolívar's lover, Manuela Sáenz tells him he ought to take time for himself.
The Ministry is now full with the Morisco refugees, who are somewhat stunned by their current situation, so very much unlike the time they come from. Lola and Ernesto discuss the refugees, and the current time.
In the past, Alonso and Pacino call to Salvador, who points out their current mission: they must save Bolívar from an imminent terrorist attack. Alonso is angry about the fact that he has to save Bolívar, pointing out that him and his fellow "Libertadores" are people of Spaniard descent, who ended up oppressing the natives.
The Ministry is a mess with all the refugees, who are being treated for potential illnesses. Then comes the Government's delegate: unknown to them, it is Bosco, the leader of the Ángel Exterminador, who brings orders to send the moriscos back to 1609. The leader of the moriscos mentions that the person who guided them through came to help them but a few days before. The Ministry declares a general alert as the guide tries to get into the place: the guide reveals himself to be one of the Sons of Padilla, who tries to blow up the Ministry with an explosive belt, but Lola kills him before he can activate it. The delegate tells Salvador he wants the refugees out in two days.
In the past, Alonso and Pacino are attended to dinner, where Alonso calls them out for their actions (that led to their being almost killed) and challenges one of Bolívar's generals to a duel. Pacino points out to him that the man he has challenged is Rafael Urdaneta, who historically will not die until 1845, but Alonso is furious.
In the present, while the moriscos are checked (and are obviously innocent) Irene (who heavily mistrusts Bosco), Ernesto and Salvador discuss the problem and the fact that they do not know what to do with them: they decide to send Lola and Ernesto to 1609 - with Velázquez (who feels guilty over how he ignored his Morisco slave Juan de Pareja and his painting ability) getting in thanks to his knowledge of the era - to meet with Philip III and gain safe conduct. The troubles increase when it turns out Elena appears on TV and mentions the refugees - and the Ángel Exterminador plots to kill Elena, before she can speak further. While Ernesto and Lola - accompanied by Velázquez - go to 1609, Irene - with some pinpoint action by Angustias - saves Elena just in time before the Ángel Exterminador's agents can murder her.
Bosco speaks with his Mooks after his failure - in front of Salvador, who notices the missing ring. Bosco tries to play Affably Evil, but when Salvador makes a modern reference, Bosco fails to understand it.
In 1826, the duel is solved peacefully when both Alonso and Urdaneta shoot in the air, but the situation does not get better: their agent-in-place has managed to record a conversation that bring proof of the conspiration against Bolívar. Alonso and Pacino tell Manuela about the conspiracy, mentioning that the peace and trade treaties they brought were but a mask to hide their true mission of protecting Bolívar.
In 1609, Ernesto and Lola meet with Philip III and request his protection for the Moriscos, but the king rejects it, saying that the Moriscos are false Christians and deserve exile and death. As they leave, they have a chance encounter with Queen Ana, clearly depressed. Lola speaks with her, mentioning her friendship with Amelia - or, as the Queen knows her, Beatrice de Spinola: the Queen was clearly affected by her leaving, as she misses her, and even more now that her pain is greater: her son, Philip, age 4, is gravely ill.
In the Ministry, Irene is in the bar with Elena, who is somewhat surprised by the events. Elena wants to leave, but Irene brings her into a conversation about Alonso: she remembers how Alonso told her about his work at the Ministry, but thinks it was just an attempt to break up with her. Salvador comes in, and invites her to follow him... to the early 20th century, to see La Belle Otero, shocking an initially disbelieving Elena, while Salvador points out she ought to have suspected something earlier. Salvador impresses upon her the need to keep the reality of the Ministry quiet, lest she gets in further danger.
Just then, Ernesto, Lola and Velázquez return from their mission and report their failure (at least, they know that kings after Philip II did not know about the Ministry until the 19th century). However, Velázquez makes a chance comment about Philip III being ill at around age 4 and being healed by a Morisco doctor - which, by chance, is Habib, the leader of the Morisco refugees.
In 1826, Manuela reads a book aloud for Bolívar, and adds some powder to an infusion she gives him: the Libertador falls asleep almost immediately. Just then, a group of members of the Ángel Exterminador, led by a man called Arteche, enters the palace where Bolívar lives, knocking out or killing the guards, while Arteche uses the distraction to reach Bolívar's room. Manuela steps on the way, but Arteche just slaps her.
In the present, Maryam, one of the Morisco women, who was heavily pregnant, starts to give birth, while a terrified Angustias asks for help.
In 1826, Arteche enters Bolívar's room and shoots at him - or not, because Bolívar has been moved away, and Pacino shoots at the man's hand, and then the leg, but somehow this does not cause him much harm. Arteche tackles Pacino and begins to throttle him.
In the present, Irene (who has experience in helping give birth) and Angustias aid Maryam in the birth of a healthy baby boy she names after her husband, who was Habib's nephew.
In 1826, Pacino manages to make Arteche let him go by kneeing him where it hurts the worst and manages to grab his gun. Arteche makes a move to attack Pacino, who shoots him again, but with little effect. It comes down to Alonso - who has managed to help stop the attack by the other Ángel Exterminador's mooks - to knock Arteche out, although it takes a couple of attempts before he is finally left unconscious. Bolívar, after he awakens, thanks Manuela, Alonso and Pacino for saving him.
In 1609, Ernesto and Lola convince the King to allow safe passage for the Moriscos in exchange of Habib healing his son. Philip III immediately recognizes the man who once saved his life, and the future Philip IV is successfully healed - with some modern aid. The refugees are escorted to Valencia, where they will be allowed to travel by sea towards Italy.
All the missions solved - although Bosco barely hides his disappointment with Bolívar's survival - Salvador reminds him he made a promise to help increase the Ministry's budget. As soon as the man leaves, though, Salvador tells Irene he now shares her suspicions against Bosco. The main mystery right now, though, is Arteche, the man Alonso and Pacino captured: keeping him sedated takes triple the usual dose, and the injuries from the bullets Pacino shot at him (which are now burned and half broken) have rapidly cicatrized.
But there is still another issue: Irene brings in Elena, so she can talk with Alonso. In order to show her what is happening, he takes Elena to 1575, a few years before his death... and shows her Blanca, his wife from his pre-Ministry life. Elena is left shocked at the physical similarites between herself and Blanca.
And Pacino visits Marta... who awakens from her coma... but does not recognize Pacino.
