One night, Hubie and Marina's engaement emerald begins to glow ominously and our heroes suddenly wake up in Africa. Yen Sid's face appears in the pebble and tells the team that they are many years in the past and a mission has been laid before them. Only after their task is complete will they return to their timeline. Also they must not reveal that they are from another time. Shortly afterwards the group meet Timon the meerkat and Pumbaa the warthog who are looking for a dream home. Thinking this may mean something, Hubie and his friends join them.

In the Pride Lands of Africa, a lion rules over the animals as king. The birth of King Mufasa and Queen Sarabi's son Simba creates envy and resentment in Mufasa's younger brother, Scar, who knows his nephew now replaces him as heir to the throne. After Simba has grown into a young cub, Mufasa gives him a tour of the Pride Lands, teaching him the responsibilities of being a king and the Circle of Life. Later that day, Scar tricks Simba and his best friend Nala into exploring a forbidden elephant graveyard, despite the protests of Mufasa's hornbill majordomo Zazu. At the graveyard, three spotted hyenas named Shenzi, Banzai and Ed attack the cubs before Mufasa, alerted by Zazu, rescues them and forgives Simba for his actions. That night, the hyenas, who are allied with Scar, plot with him to kill Mufasa and Simba.

The next day Scar lures Simba to a gorge and tells him to wait there while he gets Mufasa. On Scar's orders, the hyenas stampede a large herd of wildebeest into the gorge. Mufasa rescues Simba, but as Mufasa tries to climb up the gorge's walls, Scar throws him back into the stampede, where he is trampled to death. After Simba finds Mufasa's body, Scar convinces him he was responsible for his father's death and advises Simba to flee the kingdom. As Simba leaves, Scar orders Shenzi, Banzai and Ed to kill the cub, but Simba escapes. That night, Scar announces to the pride that both Mufasa and Simba were killed in the stampede and steps forward as the new king, allowing a pack of hyenas to live in the Pride Lands.

After running far away, Simba collapses from exhaustion in a desert. Hubie, Marina, their friends and Timon and Pumbaa find him and nurse him back to health. Hubie realizes who he is, but pretends he doesn't, under Yen Sid's wishes.

Simba subsequently grows up in the jungle, living a carefree life with his friends under Timon and Pumbaa's motto "hakuna matata" ("no worries" in Swahili). When he is a young adult, Simba rescues Timon and Pumbaa from a hungry lioness, who turns out to be Nala. She and Simba reconcile and fall in love. Nala urges Simba to return home, telling him the Pride Lands have become a wasteland with not enough food and water. Feeling guilty over his father's death, Simba refuses and storms off, leaving Nala disappointed and angry. As Simba exits the jungle with Splatter Phoenix, they encounter Mufasa's mandrill friend and advisor, Rafiki. Rafiki tells Simba that Mufasa is "alive" and takes him, along with Splatter to a pond. There they are visited by the ghost of Mufasa in the sky, who tells him he must take his rightful place as the king of the Pride Lands. Simba realizes he can no longer run from his past and goes home. Splatter finally begins to realise what their task was and tells the rest of the team. They, along with Nala, Timon, and Pumbaa join Simba, and agree to help him fight.

At the Pride Lands, Simba sees Scar hit Sarabi and confronts him, but Scar taunts Simba over his "part" in Mufasa's death, despite Splatter trying to defend him. However, when Scar pushes Simba to the edge of Pride Rock, he reveals that he killed Mufasa. Enraged, Simba roars back up and forces Scar to reveal the truth to the pride. Timon, Pumbaa, Rafiki, Zazu, Hubie, Marina, Rocko, Petra, Beanie, Timmy, Pikatwo, Bonkers, Fawn, Buck, Stanley and the lionesses fend off the hyenas while Scar, attempting to escape, is cornered by Simba at the top of Pride Rock. Scar begs Simba for mercy, insisting that he is family and placing the blame on the hyenas. Simba no longer believes Scar, but spares his life on the grounds of forever leaving the Pride Lands. Scar appears to comply, but then attacks his nephew. After a fierce fight, Simba and Splatter (who rushes in at the last second) throw Scar off Pride Rock. Scar survives the fall, but is attacked and eaten alive by the hyenas, who overheard his attempt to betray them.

With Scar and the hyenas gone, Simba ascends to the top of Pride Rock and takes over the kingdom as the rain falls again. Sometime later, with Pride Rock restored to its former glory, Simba looks down happily at his kingdom with Nala, Timon, and Pumbaa by his side; Rafiki presents Simba and Nala's newborn cub to the inhabitants of the Pride Lands.

A day after the presentation, the emerald begins to glow again. Realizing their time has come, Hubie and the team say goodbye to Simba and the kingdom. As they begin to fade, Simba asks if they'll ever see them again to which Marina replies 'Only time will tell'.

Back in their original time, Hubie and the team is greeted by Yen Sid. He reveals that the mission was to teach them a lesson about the Circle of Life and Rafiki's talk of learning from past mistakes. Splatter concurs the fact that the task was mostly for her, though she tries to explain that she has learned, but admits she had never truly healed, until now. Rocko shares his first kiss with her and they, along with Hubie, Marina and the team continue for a new adventure.

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