When a group of children on a school visit to some caves return to the surface, every single person over 15 has disappeared. Opportunistic gangs roam the streets as Sadiq leads his newly-formed tribe to the safety of the City Hotel. After discovering her mum and sister missing, young scientist Kat takes charge of Liam, the boy next door. They too try to gain entry to the City Hotel, but only Liam gets in, leaving Kat to fend for herself.

The Sparticles reach the Quantum Nexus at last and the race is on to see if they can bring back the adults or stay in the world of Emperor Fizzy for ever. A curious old friend looks set to help. Dora had set up a hologram version of her self called 'HoloDora', whom she believes to be Dora's daughter and when the children are detected by 'HoloDora', she change to help them to bring back the dimension with the parents. Reese attempts to modify the magnetics of the Quantum Nexus in order to damage the machine due to her worries of connect the wrong dimensions. Reese fails to do this, as she does not know the two dimensions are connected. The wrong dimension is set to come to Earth, which results in the adults - now teenagers - arriving.

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After a year of searching for the Quantum Nexus, most of the tribe has split up. Jordan and Ami have gone to France, Kat is sorting out the nuclear power plants but everyone else reunites when they realize the key from Doomsday Dora fits into a stone head. But the head is in a stadium owned by Fizzy and there is also the matter that there is a traitor within their tribe. Reese is captured and the dims threaten to feed her to the lion if the Sparticles lose the fight. The lion is revealed to be a hoax and Holly is revealed to be the traitor, accepting a bag of Fizzys for doing a job for Fizzy. She vows to find the Quantum Nexus first and destroy it to determine the adults never return. She and Serena take off and the Sparticles take the Stone Head back to the Spartivan and set off on a race to the Quantum Nexus.

The Sparticles, Holly and Serena all go to Peace City on their way to the River Artos. As Reese is being pulled through as she tells Sadiq, "Peace City might be the Quantum Nexus." Holly and Serena lose the sword (which is taken by Rocky in disguise). Fizzy puts up wanted posters for the Sparticles. Reese meets another person who has special powers named Huen. Tensions rise as Ernesto and Callum arrive. As Holly and Serena exit, Holly spots the sword and shows Serena it hadn't dissolved in the acid bath. She grabs it and they decide to head off for Water Mint Mill.

The Sparticles find the stone which opens the Quantum Nexus but Jeffrey gets poisoned by itcyflax flower so therefore the Sparticles go to a castle to get a treatment but Holly messed up their car so Holly and Serena have to give them a ride to a castle that has the cure but the Sparticles and Holly and Serena soon get caught up in duels when they lose their sword.

The Treasure Hunt is coming together with the discovery of another vital clue in the race to the Quantum Nexus, but the return of Ernesto leads to questions - exactly whose side is the Rebel on? Later on, Reese sees Muna and it is revealed that Muna came back in limbo at the Sparticle Mystery. Muna also tells Reese that it is dangerous to realign the 2 worlds as there are many more dimensions that could destroy them. Later on, it is discovered that Sadiq tells the other Sparticles that Serena is a double agent.

A trail is laid for the Treasure Hunt, but the two competing teams start falling apart. Loyalties become strained and old rivals become new friends. Holly understood the last letter of the last episode and is teamed up with Serena. Holly soon discovers that Serena is on the Sparticles' side rather than hers. Holly leaves her hurt by the riverside (Serena was hurt after a cut from the sword) and teams up with Ernesto and Fizzy and is soon joined by Reese to destroy the Quantum Nexus.They now make a group called The Freedom 4. The Sparticles soon find Serena using the tennis balls to guide them and discover the others are already ahead in the Quantum Nexus. Jeffrey stays behind to help Serena while the others go ahead and discover the Quantum Nexus.

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The Sparticles and Holly and Serena bump into a circus tribe while searching for the white horse. For Serena, will it be a happy reunion with her sister?

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The Sparticles travel to an abandoned mill where a supposed creature has been eating children. There, Tia and Jeffrey's relationship comes under strain and Rocky shows his true colors as he snatches the necklace Tia gave to Jeffery and throws it in the River blaming Jeffery for the incident. The Sparticles get their next clue, which leads them closer to the Quantum Nexus.

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The Sparticles and Holly and Serena arrive at the museum where the stone head belongs and plan to decode the message on the Stone Head, but the Sparticles get caught up in a plan with another tribe, the Featherheads to raid the museum in order to get gold to melt down to turn into Fizzys to use to buy fuel.

A tribe of Traders lock up the Sparticles and accuse them of stealing their shipment which was to be given to Fizzy. They soon discover that the shipment was chocolate and that Fizzy is going to make an army using these. Serena and Holly are then captured and put into a room as the Traders thought they were Sparticles. After an escape planned by Frankie, Liam and Reese, they tried to rescue the others but were unfortunately captured again but Frankie and Liam escaped and found the balaclava and shipment and they discover that it's Skinny as he was 'sick' of taking orders from his boss. He is then arrested by Callum for breaking one of the rules but soon freed to help the Sparticles. Rocky stayed behind to help the Sparticles rather than Callum. Fizzy turns up and the chocolate is melted and Rocky tells to stay off the Quantum Nexus and the Sparticles to get chocolate and biscuits and it was agreed except of Fizzy who was frustrated.

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Callum has formed a biker gang and has designs on the City Hotel as the gang's new hang out. He befriends Kat as she might be useful to his success. However, Kat is on her own mission to find out what has caused the disappearance of all the adults and encounters Reese at the City Library. Reese insists she can see the adults and feels she has found an ally in Kat. Meanwhile, inside the hotel, Holly is left wondering where her parents are.