Three students are chosen from the Phai Zhuq academy by Master Mao to protect the evil Dai Shi's concealment. After an altercation, Jarrod is kicked out of the academy and the cub Casey is put in his place. Jarrod objects and leads to releasing Dai Shi and destroying Master Mao's physical form. The trio are sent to their new master, the mellow R.J. , the owner of a pizza place. He alone has the tools for them to protect the world from Dai Shi.
Camille steals the Spirit of the Buffalo from a monk and gives it a Rinshi, creating Buffalord, who is formidable against the Rangers. Casey requests extra training from R.J. but, he doesn't respond well when this training just seems to just be household cleaning.
Camille brings forth the Five Fingers of Poison to increase Dai Shi's evil. Dai Shi makes his formal introduction to the rangers in the body of Jarrod, which shocks them. After Casey is beaten up, Lily has a nightmare that might spell Casey's end. She decides to take one of the Poisons on her own.
Gakko, one of the Poisons, can walk on walls, which he calls 'his world.' Theo is beaten by Gacko and doesn't take it well, it diminishes his self-confidence. Casey and Lily respond to another attack from Gakko, while R.J. trains Theo in forest to regain his confidence.
Theo can't deal with how Lily is so chummy with Casey. Stingerella attacks with dangerous dance moves. Toady, who loves Stingrella, mistakes Theo kissing her and attacks. The Rangers manage to beat Stingerella, but with Camille's encouragement, Toady shows off and wins Stingrella's love, becoming a powerful team. Because of the tension between Casey and Theo, the rangers can't operate the new Claw Canon to defeat the lovebirds.
Camille finds out Naja is plotting to overthrow her beloved Dai Shi. She risks her life, taking on her own kind of training in order to protect Dai Shi. RJ goes fishing and leaves the pizza shop to Casey, who rather leave his responsibility to everyone else. Chaos ensues and Fran quits. Can the Rangers get the shop functional before RJ comes back? Will Camille survive?
The Rangers can't manage to defeat the Pangolin, so they must seek out the only weapon that can defeat him: the Jungle Mace. Unfortunately, the owner of Jungle Mace, Master Phant has left Pai Zhuq and doesn't want to teach, because he no longer feels needed. Lily refuses to leave until she is taught the way of the Elephant, in order to save the world.
In order to obtain a kite he wants to buy, young Josh tries stealing from the pizza shop. Casey catches him and teaches him the importance of earning things for himself. Jarrod releases Carnisoar, the Sky Overlord and he erases all his good deeds from his past in order to rid him of his humanity. Camille meanwhile sends Slickagon to make things slippery for the Rangers.
Theo's multitasking is not working and Master Swoop, a blind Pai Zhuq master, intends to show him the way of the Bat Spirit in order to focus and defeat Carnisoar's personal warriors Bai Lai and Carden, who intend to collect energy and use it against humanity.
Camille is temporarily kicked out of the palace and under disguise at the Pizza place, Lily is sympathetic to her and inadvertently gives her the idea to raise another Overlord, Jellica. Jellica is more than Camille can handle, as she intended her to be Dai Shi's master, but she orders Camille to do away with the only one that ever showed her kindness... Lily.
Casey is eager to meet his new master but RJ is not for it, as the master is his father Master Finn, who he has not spoken to in years. Jellica commences her training of Dai Shi as she sent Camille with Crustaceo, who can possess anything, even Master Finn's shark spirit!
The trio feel unstoppable after defeating another of Camille's warriors, but Dai Shi kicks their butts with his new level of power. RJ offers his life to spare his students lives and is taken to Dai Shi's temple, leaving the Rangers alone and feeling helpless.
The Rangers are taken to the Spirit world by their old master, Master Mao to be trained by three defunct masters. Jarrod prepares a battle arena to fight RJ to death. The Rangers must face their fears to gain new power, while Fran finds out who they really are.
Everyone is still making fun of Lily for being too nice. After a battle with Porcupongo, Lily starts shows her bad side. Fran confronts her when she refuses to help her friends when they go against a werewolf and after a tussle, Frans finds that Lily has been affected by one of Porcupongo's quills.
The werewolf Theo and Casey fought turns out to be RJ, whose animal spirit became out of control due to his last battle with Dai Shi. RJ learns to lean on his friends and not run away from them when he has a problem. Meanwhile, Dai Shi is overthrown by Grizzaka, who refuses to take orders from any human.
Now that RJ is a Ranger, Casey feels RJ is taking over as leader. Casey now feels as he did when he started as a cub at the Pai Zhuq Academy. Grizzaka, who possesses the incredible power of Zocato, releases two warriors from his vast army to lay waste.
RJ's werewolf side arises again after an altercation between Dai Shi and Grizzaka during a Megazord battle, cause RJ to turn the Wolf Pride Megazord against the Jungle Master Megazord. When he is taken down, he inadvertently saves Flit and Flit wants to repay his new friend. Flit was once a human and cursed by Camille long ago and she has the key to tame the beast inside RJ.
Dominic, an old friend of RJ from Pai Zhuq, arrives to the Jungle Karma. The others don't warm up to him instantly as he seems not take things seriously. He has been seeking his purpose in life, which he has now found as the Rhino Ranger.
Jarrod needs the Control Dagger in order to tap into the vast power of the Rhino Nexus. Dominic has a dream, which in reality is a memory of when Master Mao giving him the Control Dagger. Dominic and Theo go in search for the dagger, but they are not the only ones after it. Meanwhile, the others fight against the crazy Whirnado.
With Control Dagger in hand, Dai Shi aims to unlock the Nexus for himself, but has the Overlords in his way. The Rangers refuse to let such power fall into the hands of the Overlords or Dai Shi. Having searched all his life for his destiny, Dominic isn't about to let the anyone stand in his way. With the help of his friends, Dominic is able to unlock the power of the Rhino Steel Megazord.
The crystal eyes hold the power to bring back the notorious Phantom Beasts. Our heroes must retrieve five of these eyes, that are in the hands of Dr. Jennings, before the Over Lords resurrect such evil beasts. Dr. Jennings refuses to let go the eyes which her deceased father sought his entire life. Meanwhile, Grizzaka releases his onslaught upon the world.
Lily trains Master Phant's niece Gabby for a dance competition but her fears are what holds her back. The Phantom Beasts have been brought back to life. Dai Shi has them prove their loyalty by capturing the three masters. The Phantom Beasts capture the masters and use the masters to create the Spirit Rangers.
The Phantom Beasts control the masters and call forth the Spirit Rangers. RJ makes a device that will momentarily stop the Spirit Rangers. Theo's twin brother, Lewin, comes into town and reminds Theo of their conflicts. Lewin is mistaken for Theo and captured by Dynamir, it is now up to Theo to save the day.
The Spirit Rangers could be the end of our heroes if something isn't done. RJ takes the risk of destroying his father by refining the Claw Cannon. Trusting his instincts, he finds that his dad was prepared if this should happen. Together with the help of his dad, RJ saves the other Masters from the grip of destruction.
A Rinshi was sent to fiddle with the Rangers' monitor and the Rangers sans RJ are sucked into a game show starring a colorful host and Camille. Asked questions about past events in their journey, if they answer wrong, they are in danger of being canceled.
Whiger steals some of Casey's Tiger spirit and because of this, Dai Shi becomes the Phantom Beast King and appoints Camille a Phantom Beast General, which angers the others. Weakened from the loss of his spirit, Casey must summon all the energy he has left to stay alive, along with some unexpected help from a young student.
For his failure for not destroy Casey, Dai Shi strips Whiger of his power and banishes him. Casey shows his kindness to Whiger even though they were just battling. Whiger rethinks which side he should be on as he fades away. Whiger helps Casey save his friends who have been captured along with all the other people in giant rattraps.
Grinder is sent by Camille to steal a clone formula from the smart and beautiful scientist who Dominic protects and develops feelings for. Dominic tries to win her over but makes some missteps and there is trust issues. She has the key to defeating the multiple Grinders that ravage the city and give the Rangers their money's worth. Scorch works as a secret informant in hopes to ruin Camille's plan.
The day has come for the three to get their master stripes. Lily and Theo pass the test but Casey doesn't as he didn't seem to know what he was doing. Scorch and Snapper sends the three remaining Phantom Beast Generals after Camille. Casey comes across Jarrod saving Camille and he begins to think that Jarrod might still be able to be saved. The others don't believe him and tell him that all that matters is destroying Dai Shi.
Although no one believes that Jarrod still lives inside of Dai Shi including Master Mao, Casey bravely enters Dai Shi's palace to save Jarrod. In an epic battle between Dai Shi and Casey, Jarrod manages to break free of Dai Shi. Camille helps Jarrod and the Rangers in escaping Dai Shi and defeating the remaining Phantom Beast Generals. For following his heart, Casey gets his Master Stripes.
Scorch starts a new Beast War with the Rinshi and the three Rangers go to Jarrod and Camille and ask for their help. Dom and RJ were outnumbered and the three older masters came to lend a hand. Dai Shi opens up a portal to the Spirit World and resurrects all his fallen warriors. The rangers do their best to battle evil. Jarrod finally decides to join them as well. It is left to the three chosen guardians to destroy Dai Shi forever.