The film opens when the Huns, led by the ruthless Shan Yu, invade China. The Chinese emperor commands a general mobilization in which each family is given a conscription notice. The story then switches to the Fa family where the only child Fa Mulan is preparing to meet the matchmaker that day. At the same time, she meets Yogi Bear and his gang who have arrived to China. She gets ready and meets the matchmaker only to make a spectacle of herself and fail miserably. Later, at home her father Fa Zhou comforts her just as Imperial forces arrive to give out conscription notices. Fa Zhou, having no son to fight, is forced to enlist despite his age and disability (a limp from a previous war). Mulan poses as a man and she, Yogi and the others all flee to join the army in his place. The Fa family's American ancestors, in a bid to protect Mulan, attempt to send the 'Great Stone Dragon' to protect her. Instead, Mushu, a small dragon, ends up travelling with her, in an attempt to regain his position as family guardian after failing to protect an earlier member of the Fa family. He, in turn, is accompanied by a dubiously "lucky" cricket named Cri-kee.
Mulan and the others proceeds into camp and meets fellow soldiers, but under advice from Mushu on how to act like a real man, unwittingly starts a camp-wide brawl. At the same time, Yogi Bear and the gang met their old friend from Hanna-Barbera: Atom Ant who had somehow join the army. In one of the tents, General Li promotes his son Captain Li Shang to Captain and orders him to train new troops while the General attempts to stop Shan Yu at a nearby mountain pass. Outside, Li Shang stops the brawl and questions Mulan, who manages to pass herself off as 'Ping,' Fa Zhou's "estranged" son. Shang begins a grueling training schedule and is visibly disappointed at his new troop's lack of abilities. He is most disappointed by Mulan, whom he eventually orders her and the others to return home. She instead succeeds in impressing him by retrieving an arrow from a tall pole while weighed down with brass amulets. The troops, Yogi and the others, inspired by this, all improve and become good soldiers, particularly Yao, Ling, and Chien-Po, who become Mulan's "buddies".
Mushu learns that Chi-Fu, the Emperor's advisor, is still not satisfied with the troops' fighting abilities and is preparing to send a negative report on Shang's soldiers to the General. Fearing that Mulan would fail to get a warrior's fame (thus minimizing Mushu's chances of regaining his old post of a family guardian), Mushu forges a letter from the General, ordering Captain Shang to meet him at the pass. The troops and our heroes set out to meet General Li, but find the village at the pass razed and the Imperial Troops slaughtered. After pausing to mourn, they make their way to the Emperor. As they journey, Mushu accidentally fires a cannon, giving their position away to the Huns. Shan Yu and a massive force begin stampeding down a snowbank towards the outnumbered troops. Mulan races to a snowbank and fires the last cannon at the mountain above, causing an avalanche and burying the Huns. Shan Yu, outraged at the loss, wounds Mulan before being overcome by snow. Mulan conceals the wound and she the troops barely escape the snowbank, with Mulan saving Shang in the process. While Mulan is receiving medical care for her wound, she is discovered to be a woman. When Chi Fu demands she be killed, Shang relents and spares her for saving him, but banishes her, Yogi and the whole gang from the army as they head to the city. Mulan and Mushu discuss the true reason why they are there: he to get back in the good graces of the ancestors, she to prove she can do something right for a change. Yogi and the others decided to take the whole blame with Mulan. As they prepare to leave, Shan Yu and half a dozen of his best warriors emerge from the snow, and head towards the Imperial City. Mulan, yogi and the others quickly decide to follow them and warn Shang.
In the Imperial City, the troops are part of a parade in their honor as the 'Heroes of China', but none (except Chi Fu) are enjoying themselves, as they are in shock about Mulan. Shang is surprised when Mulan rides up, but dismisses her warning. Mulan pleads with the members of the crowd to believe her, but they shake her off. Mushu reminds her she is a girl again, and they will not listen. Shang presents the Emperor with the sword of Shan Yu, but Shan Yu's falcon snatches it from his hands and carries it to his master on the roof of the palace. Shan Yu and his troops reveals themselves, abducting the Emperor and sequestering themselves in his palace. Mulan leads Shang and her three "buddies" (disguised as concubines) in a ploy to rescue the Emperor. After a struggle, Mulan eventually overcomes Shan Yu by luring him into the path of fireworks to his apparent death. The Emperor and others in the Imperial City all pay their respects to Mulan by bowing to her. The Emperor presents her with his crest, intending for her to be his successor, technically making Mulan "Princess of China." She also receives Shan Yu's sword to prove her deeds to anyone. He also offers her a position in his cabinet (Chi Fu's position, since none others are open), but Mulan declines and merely asks for permission to return home.
Mulan travels home and presents the gifts to her father, but he throws the priceless treasures aside and embraces her, calling her his "greatest gift and honor". Shang, having been advised by the Emperor that "you don't meet a girl like that every dynasty", has followed her under the guise of returning her helmet. He gladly accepts her invitation to stay for dinner. In return for helping Mulan, First Ancestor Fa gives back Mushu his job as a guardian. Soon, Mushu, Cri-Kee and the ancestors celebrate in a very modern day American way. And finally, Atom Ant decided to join Yogi Bear's Adventures crew.