The film picks up about six months after the first one with Grindelwald escaping his transport from prison in America to his trial in Europe. However, the man they believed to be Grindelwald was actually Queenie's boss Abernathy whom he'd swayed to his side and swapped places with. Grindelwald saves Abernathy and heads off to Europe. After another time skip of about three months, we find Newt has published his book in the interim. When we first see him, he's at the Ministry of Magic for a meeting to get his passport reinstated when he runs into his old friend Leta Lestrange. Leta's engaged to his brother Theseus, the head Auror. Though Theseus loves him, he is frustrated by Newt’s refusal to take a side and inability to hold his tongue. Theseus asks Newt to keep an open mind and be respectful in order to get his passport back. In the meeting, the Ministry officials tell him that Credence survived the first film and that he's in an unknown location in continental Europe.
They offer him his passport back if he'll go to work for his brother and join the hunt for Credence which Newt flatly refuses. Theseus runs after Newt and tells him to be careful because the various Ministries don't believe his reason for being in New York and that he's being surveilled. After the meeting, Newt meets Dumbledore whom we find out was the friend that tipped Newt off about the abused Thunderbird. He tells Newt that he's always had a predilection for magical birds due to a family story about phoenixes and that's why he got in touch with Newt. Newt doesn't buy it for a second and presses him on the fact that he knew Grindelwald was in New York and he knew Newt would have to travel through the harbor to get Frank to Arizona. Dumbledore acquiesces and tells Newt that Grindelwald, a seer, had had a vision many years ago of using an obscurial to kill him. Dumbledore says he can't fight Grindelwald but he wants Newt to go to Paris to find Credence, whom he believes can be cured of the obscurus if he finds his real family. He reiterates the rumor that Credence is actually Leta's half-brother Corvus V who was long believed to be dead. Newt refuses to go since he doesn't have a passport.
Newt is working in his home with his assistant Bunty when he finds Queenie and Jacob at his doorstep. Queenie tells him they've kept their relationship in the interim, she and Tina are fighting over it, and that they've come to Europe to get married. She also tells him that Tina is dating someone else because she read an incorrect article about his book release that said he was engaged to Leta instead of Theseus. Newt realizes that something is off with Jacob. Queenie had bewitched him into coming to the UK to get married. Newt undoes the curse and Queenie and Jacob have a fight that ends with Queenie going off to find Tina who's in Paris on (what Queenie believes is) an official assignment. After Newt learns that she's in Paris, he agrees to go and he and Jacob take an illegal portkey across the channel to find them. Grindelwald is also in Paris trying to find Credence with his minions in tow. They kill a Muggle family and use their apartment as a makeshift base.
In Paris, Credence is working at circus with his friend Nagini (who at this point is still able to control her transformation into a snake) and the two of them have been trying to find his birth mother. When they think they've found her in a woman named Irma Dugard, they escape. Irma tells him that she wasn't his mother but rather a servant and right as she's about to tell him more about his family, she's killed by one of Grindelwald's minions. Tina, who was at the circus the night they escaped and wasn't there on official business, meets a man there named Yusuf Kama who is also hunting Credence. Newt and Jacob use Yusuf to track Tina, who's been imprisoned by him in the meantime. When they catch up to Yusuf and Tina, Yusuf imprisons them as well and explains that he'd made an unbreakable vow with his father to kill Credence, whom he also believes to be Corvus V. Credence and Nagini are also visited by Grindelwald who invites them to his upcoming rally.
Queenie gets to the French Ministry in hopes of finding Tina but since she wasn't there working officially for the Ministry, she is unable to find her. She leaves the Ministry distraught and gets overwhelmed trying to find Jacob's thoughts in a crowd of French speakers whose thoughts she can't understand. She begins sobbing in the street and is quickly helped by a seemingly kind woman who offers to take her home for a cup of tea and to get out of the rain. Once Queenie has calmed down, she realizes the kind woman wasn't helping her for altruistic reasons. She tries to leave, saying Tina is waiting on her and is probably worried sick but the woman won’t let her. She's Grindelwald's right hand woman, Vinda Rosier, and has brought her to the apartment to recruit her to their cause. Grindelwald comes out and gives Queenie his "greater good" spiel before he lets her go.
Back in the UK, a group from the ministry (including Theseus and Leta) barges into Dumbledore's class demanding that he fight Grindelwald. When Dumbledore says he can't do that, Theseus' boss Torquil Travers puts him on house arrest and bans him from teaching Defense Against the Dark Arts. Dumbledore warns Travers that fighting Grindelwald's violence with violence is giving him what he wants but he doesn't listen. Once Travers storms out, he pleads with Theseus to trust him that if they are going to break up the rally, don’t rise to his rhetoric. Theseus does take the advice to heart. Dumbledore finds Leta in an old classroom, the two of them talk about the death of their siblings and he asks her if she wants to confess anything but she refuses. He also tells her that she's a good person no matter what she thinks and that she needs to learn to forgive herself for whatever happened.
Newt and Tina infiltrate the French Ministry of Magic for documents to confirm Credence's identity, but are discovered by Theseus. Once they escape, Tina and Newt clear the air about the misunderstanding with the magazine and they bump into Leta who's also there looking for the documents. They find out the documents are in the family tomb and when the three of them get there, they find Yusuf, Jacob, Credence, and Nagini, with the former holding the latter three at wandpoint. Yusuf says that he's sorry he has to do it but he must kill Credence because Corvus IV imperius-ed his mother into marrying him, got her pregnant, and then she died giving birth to Leta, his half-sister. Kama Sr swore his son to get revenge on Corvus V for this. Leta stops him and says that Credence isn't Corvus because Corvus had for sure died as a baby because she killed him. She explains that when her father found out about the vow, he sent them to America with Irma so Corvus could be adopted by Mrs Barebone. Corvus wouldn't stop crying on the ship, so she swapped him with baby Credence next door who was quiet. That very night, the ship sank before she could switch the two baby boys back, and Credence's aunt died trying to save the baby who was actually Corvus (who drowned that night) while young Leta sat in the lifeboat holding the real Credence. She kept this a secret ever since, only maintaining publicly that her brother was dead.
They go to the rally where Queenie is among the attendees and Jacob is looking for her. Grindelwald shows a vision of a future global war, and rails against the laws prohibiting them from preventing such a tragedy. Theseus and the Auror show up at the rally and even though he's trying to take Dumbledore's advice, a twitchy member of the squad gets goaded into killing an attendee. Grindelwald prompts his followers to spread his message across Europe, and conjures a ring of blue fire that kills the retreating Aurors and that only his most loyal followers can safely cross. Grindelwald tells Credence if he joins him, he will tell him who he really is. Nagini tries to stop him from going, saying that the people he’s joining hunt people like them for sport. However, he and Queenie cross the fire, while Leta sacrifices herself (while telling Newt and Theseus that she loves them) so the others can escape. As Grindelwald and his followers depart, the remaining wizards and immortal alchemist Nicolas Flamel extinguish the fire. Newt hugs a distraught Theseus and tells him he's ready to join the fight.
Newt, Tina, Yusuf, Nagini, Jacob, and the Aurors go back to Hogwarts so Newt can talk privately to Dumbledore, whom Theseus lets off house arrest. Newt gives him a pendant containing a blood pact stolen by the niffler that Grindelwald and Dumbledore made in their youth that prevents them dueling each other; Dumbledore believes it can be destroyed. At Nurmengard Castle, his Austrian base, Grindelwald presents Credence with a wand. He tells him his alleged birth name, Aurelius Dumbledore, and gives him a phoenix while saying his "brother" is trying to kill him.
