The film opens with Hiccup (Jay Baruchel) saying how his village of Berk has since welcomed the presence of dragons, using them as pets, or for sports, such as dragon racing. All the vikings in the village gather for a game where Hiccup's friends compete with their dragons by scooping sheep and throwing them into nets. The twins Ruffnut (Kristen Wiig) and Tuffnut (TJ Miller) are leading with their Hideous Zippleback, Barf and Belch. Hiccup's girlfriend Astrid (America Ferrara) is in second place with her Deadly Nadder, Stormfly. Snotlout (Jonah Hill) is on his Monstrous Nightmare, Hookfang, and Fishlegs rides his Gronckle, Meatlug, but both of them have since become infatuated with Ruffnut. Astrid swoops down to catch the black sheep to win the game. Hiccup's dad Stoick (Gerard Butler) and his friend Gobber (Craig Ferguson) keep an eye out for Hiccup, who is nowhere to be seen.
Hiccup is flying with his Night Fury, Toothless, across the sky, high over the clouds. When they get high enough, Hiccup drops himself from Toothless's back and spreads the wings on his flight suit, soaring right alongside his dragon. He nearly crashes into a stone column until Toothless hits it with his fire and saves Hiccup. They crash land onto an uncharted cliff, prompting Hiccup to add it to his map. They are joined by Astrid and Stormfly. Astrid asks Hiccup why he wasn't around, and he admits that he's tried to avoid talking to his dad about succeeding him as chief of Berk. Astrid is excited at the prospect, but Hiccup doesn't feel that he has what it takes to lead the village. Astrid is confident that he does. They then spot a large cloud of black smoke in the distance and fly off to investigate.
Hiccup, Astrid, and their dragons come across an island surrounded by ice. A group of men spot them and launch a net, trapping Stormfly. Astrid falls off, but Toothless grabs her. The leader of the trappers, Eret (Kit Harington), comes out to introduce himself, stating that he is capturing dragons for his employer, Drago Bludvist. He accuses Hiccup and the other dragon riders of coming near their fort and taking their dragons, though Hiccup has no idea who could be behind that. Hiccup uses his fire sword to free Stormfly and get out of there.
Upon returning to Berk, Hiccup warns Stoick about the dragon trappers. When he mentions Drago Bludvist, a horrified look falls over Stoick's face. He rushes to warn the others and then tells Hiccup that Drago is a ruthless madman. Stoick gets everybody to gather together to prepare for trouble.
Hiccup and Astrid ride their dragons to find the dragon trappers on their ship. Hiccup surrenders himself and Astrid, along with Toothless and Stormfly, in an attempt to join Eret so that he may reason with Drago. Stoick finds him and rides on his own dragon, Skullcrusher. He tells Hiccup that years ago, during a meeting of chieftains, Drago Bludvist (Djimon Hounsou) sought to aid everyone and protect them, but only if they bowed to him. Everybody laughed him off, so Drago set off an armored dragon and had all the chiefs burnt, with only Stoick making it out alive. He tries to get Hiccup to come back with him, but Hiccup instead flies away with Toothless.
Up in the clouds, Hiccup and Toothless are spotted by a masked figure riding a dragon. They take Hiccup, and Toothless, unable to fly without his rider, falls into the icy ocean. He tries to swim out, but is taken by other dragons. Both he and Hiccup are brought into a cave. Hiccup finds himself surrounded by other species of dragons that he's never seen before. He takes out his sword, which he uses to ignite flaming gas. The other dragons and the masked figure appear impressed. Hiccup reaches his hand to touch one of the dragons, but the masked figure steps down and stands before Hiccup. Noticing a scar on his chin, the figure takes off the mask to reveal a woman named Valka (Cate Blanchett). She recognizes Hiccup, but he doesn't know who she is. When he asks her if he should know, she replies, "No. You were only a babe. But a mother never forgets." A stunned Hiccup steps back.
Stoick and Gobber fly on their dragons over the icy ocean to find Hiccup. Stoick finds Hiccup's helmet in the water, and he becomes worried, but he continues to fly forward to find his son.
Hiccup follows Valka, hoping to get the answers to his many questions. She leads him to a huge nest with hundreds of dragons, including babies. Valka introduces her own dragon, Cloudjumper, to Hiccup. She explains that 20 years earlier, when Hiccup was a baby, the war between dragons and vikings was at its peak, and although Valka tried to stop the vikings from fighting, nobody listened to her. She saw Cloudjumper in her home approaching Baby Hiccup, but the dragon was not threatening. In fact, it was nurturing toward Hiccup, though it let him with a scratch on his chin (leaving the scar). Cloudjumper approached Valka, and she saw into her eyes and realized the dragon and her were not so different. That's when Stoick burst in and scared the dragon away, which carried Valka with her. Today, she has rescued countless dragons from Drago's traps, bringing them to the nest where they are all (except the babies) under the command of the gigantic Bewilderbeast. The humongous dragon rises and breathes a small patch of ice on Hiccup, which Valka says means he likes Hiccup. She continues to show Hiccup other secrets about dragons, including the protruding scales on Toothless's back that allow him to make harder turns when flying.
Hiccup's friends and their dragons sit around waiting for Stoick to bring Hiccup back. Astrid then decides to take Stormfly and lead the others and their dragons to the dragon trappers' ship. They find Eret (with whom Ruffnut is immediately smitten) and snatch him up. Astrid orders him to lead them to Drago's camp, but Eret refuses. Astrid lets Stormfly drop him, and he relents, saying he will lead them to the camp. When they get there, all the dragons except Stormfly are taken down by darts. Stormfly gets out of there as the dragon riders are captured and taken to Drago. Eret presents Drago with the dragons and the riders. Drago approaches the captured Hookfang and steps on his snout, taunting him and saying that he alone controls the dragons. Astrid tells Drago to let them go, or else the greatest dragon master (Hiccup) will come after him. Drago laughs this off. No longer needing Eret, Drago orders his men to kill him, but Stormfly swoops down and deflects the weapon hurled at Eret, only to get hit with a dart.
Stoick finds Hiccup in the caves and tries to get him out. Gobber stops him and tells him he needs to see something. He brings her to Valka, and Stoick is speechless upon seeing her again. He walks up to her, and she believes he is going to reprimand her for abandoning the village, but he softly tells her, "You're as beautiful as the day I lost you." Valka sheds a tear and Stoick kisses her.
Drago's men attempt to force Eret and the dragon riders to walk off the plank to their deaths. Eret then chooses to switch sides and fight off Drago's men, freeing himself and the riders, along with their dragons. He finds Stormfly and thanks her for saving his life, and now he is returning the favor.
Hiccup has a meal with his parents and Gobber. Stoick sings a song to Valka, and she joins in, and the two begin to dance gleefully. He invites her to come back to the village and be his wife again, and she accepts. Suddenly, they hear a rumbling. A shot is fired, hitting the ice around the sanctuary. Drago's entire army is at the shores with his own dragons under his control. The dragon riders fly and release the captured dragons, joining in the battle. Stoick and Valka hop on their dragons as well to fight Drago, as the Bewilderbeast emerges. Drago then begins screaming and waving his arm around to summon his own Alpha Bewilderbeast. The two titanic dragons duke it out, but ultimately, the Alpha impales Valka's Bewilderbeast with its tusks and is victorious. Hiccup confronts Drago and asks him why he is trying to take control of the dragons like this. Drago removes his metallic left arm to reveal the stump, stating that he knows what it's like to have his village and loved ones taken from him by dragons, and so he plans to use his Alpha to dominate all of them. He summons the Alpha forward, and with its hypnotic call, all the dragons, including Toothless, are helpless under its command. Toothless doesn't recognize Hiccup's voice, and he begins to fire up a blast from his mouth. Stoick runs in time to save Hiccup from the blast, but he is hit instead. Hiccup and Valka rush to his side, but he is already gone. After Toothless snaps out of it, he walks up to Stoick's body, and an angry Hiccup tells him to go away. Saddened, Toothless walks away and his under the Alpha's control again, with Drago riding him and taking every other dragon with him to Berk.
Stoick is given a viking's funeral. Without a leader, Hiccup feels helpless, but Valka convinces him that he has enough courage and heart to overcome his adversaries. Knowing what he has to do, Hiccup gets the riders to take the baby dragons to fly back to Berk, since they could not be controlled by the Alpha.
Drago and the Alpha have already made it to Berk, boasting of Stoick's death and enchanting the remaining dragons and freezing off most of the village. Hiccup and the others arrive, and Hiccup confronts the still enchanted Toothless. He reminds his dragon who he really is, and Toothless snaps out of it. He throws Drago off his back, and the final showdown begins. The dragon riders distract the Alpha as Hiccup and Toothless try to take him and Drago down. Toothless shoots his fire blasts at the Alpha, and he gets the scales out to stop himself and Hiccup from hitting the Alpha's tail. The Alpha freezes both Hiccup and Toothless in ice, making everyone think they are dead. As Drago laughs, a blue light glows from the ice, and the ice breaks in a powerful explosion. Toothless' back glows blue with energy, and now all the dragons stand behind him and Hiccup. Hiccup tells Drago this is how dragons are led. Together, the dragons fire off blasts at Drago and the Alpha, knocking off Drago's metal arm in the process. With one last mighty blast, Toothless fires at the Alpha and breaks off its left tusk. Defeated and alone, Drago and the Alpha retreat into the ocean. The village elder then appoints Hiccup the new chief of Berk. The vikings and dragons all bow to Hiccup. He then grabs Astrid and kisses her.
Now, Valka has rejoined the village, and Eret has become a new member as well, with Hiccup giving him Skullcrusher as his own dragon. Hiccup concludes with a voiceover, proudly declaring that although there may be armies and armadas out there trying to challenge them, there is one thing they don't have - their dragons.
The film ends with everybody surrounding Hiccup and Toothless, with Toothless letting out a mighty roar.
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