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.
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.
Having won her place in Sadiq's gang, Kat leads a team to the University to find food. Holly is taken hostage by what appears to be the only surviving adult. Reese discovers a message from Doomsday Dora, explaining her heart theory - which also explains the curious survival of the adult who is actually - at heart - a child. The need to generate new sources of fresh food leads Sadiq to free animals from a city farm. This goes very badly until Tia discovers that the cheap perfume she wears is a magnet for the nanny goat.
Doomsday Dora's message has warned the children they must reunite the two parallel worlds quickly or adults and children will remain separated permanently. The ticking clock has started. The children decide to choose who goes on the road to the Sparticle Project and who stays behind to look after Liam and Frankie by an 'Apprentice'-style challenge to source power for the City Hotel.
Jordan, Holly and Ami take being kids way too far, and nearly kill themselves on a runaway waltzer, until Muna, a child caught between the parallel worlds, comes to the rescue. The lack of grid power has led to the failure of the national water supply. Fresh water becomes the latest challenge for the Ranchers, and Frankie goes native in her attempts to find and save the precious resource.
A postcode given to Reese via Psychic Sarah at the fairground leads the Questers to a simulator where scientists were trained how to run the Sparticle Project. Ami, Jordan and Holly get trapped in the room with the prototype collider's super-cooling systems running, and the temperature is plummeting towards absolute zero. At the City Hotel, a fox has been at the chickens and the children decide to trap it. This is very tricky, but when they finally track down the animal and are set to destroy it, they decide on a better course of action.
While the team are on their way to the Sparticle Project, Ami is captured in the woods by the Water Rats - a group who love life messing around on the river. The Water Rats are at war with the Menaces - and the Questers, persuaded by Ami, decide to help. Will Ami swap the seriousness of the Quest for a kid's life of fun and games? Jeffrey is keen to help out more, but his wheelchair needs more power. Tia and Jeffrey discover a satellite communication system which allows them to send a message into the ether, asking anyone out there for the batteries Jeffrey needs. They arrive back at the hotel to a package - it's from Anita at the university and it comes with a message.
The Questers are intrigued by Head Boy Jeremy and his posh boarding school. However, they are soon locked out and Jordan has left the tribe to become a true public school believer. Camped outside the school, ex-pupils Ernesto and his rebel gang recruit the Sparticles to overthrow Jeremy's regime and rescue the Unsuitables - the 'less-than-perfects' who do the dirty work for Jeremy and his cadets. The Ranchers at the City Hotel work out how to bypass the first door at the Sparticle Project. Working with Anita at the university, they come up with an ingenious solution, but now they need to get the key to the Questers out on the road.
Jeffrey is proud of his abundant garden, but when hungry waifs turn up at the hotel, he finds himself at war. The Questers on their way to the Sparticle Project discover a bucolic village run on communal principals. Reese 'sees' Muna again and with the help of Tamsin, one of the village kids, Kat figures out that the wormhole events are occurring at points where leylines intersect. Some of the Questers, however, have been caught red-handed stealing food and are made to stand trial in the children's court where the issue is whether stealing to survive is justified.
The Ranchers have invited a tribe of seriously idle girls into their hotel. As they take advantage, the Ranchers are forced to fight back - but who will be turfed out of their home? Holly is anxious when she realises the journey to the Sparticle Project is coming to its conclusion. She leaves her fellow Questers trapped in an underground nuclear bunker, but there is another force at work. A computer who thinks there has been a nuclear war competes against the ingenuity of the children in a battle of wits.
The Questers discover an alarming new threat. Without the adults, and the automatic cooling systems, the world's nuclear power plants are melting down and threaten to destroy the earth. The Questers have to get a message to the adults - but how? Callum arrives to collect the key to the Sparticle Project from the Ranchers, only to discover them homeless. Tia and Jeffrey don't trust Callum after past encounters. But the key has been lost and sold and Callum is the only hope to getting it back and to reuniting them with their friends.
Ami lapses into a diabetic coma and the Questers rush him to hospital to find some insulin. Switching a generator on in the hospital may just have cost one baby his life. The kids running the hospital need fuel to run the generators to keep the babies alive. Aware of the ticking clock to get to the Project but desperate to put things right, the Questers undertake a dangerous mission as a solution. They have to distract a German shepherd dog who is guarding a yard full of petrol lorries. Meanwhile, it is Tia's fifteenth birthday. Will she be transported to join the adults in a parallel dimension?
The Questers and Ranchers are reunited at Black Tor Mine where the adults were separated from the children by the machine of the Sparticle Project. But another tribe - the Mystic Moles - the children of the scientists working there, won't let anyone through the doors. Tia and Jeffery share a kiss. Callum arrives with the dictator and Kat kisses him as a thanks. The Sparticles face a series of challenges before they get to their greatest obstacle. Although they are successful reuniting the worlds, before the reunification stabilises, Kat stops the beam to save Reese's life. This disrupts the realignment process and the two world split again. Doomsday Dora tells the Questers to travel to the Quantum Nexus (hinting a second series). Just before Kat's dad disappears, he gives her a code to shut down the world's nuclear power plants.
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 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. Holly and Serena break into the museum and use the decoder to translate the message on the Stone Head, which was written on a piece of paper that they stole from Reese. While Jeffery and a member of the Featherhead work on a machine turning waste into fuel, the remaining Featherheads rob the gold from the museum, including the Decoder. Reese attempts to get it back but is caught in the diggers bucket and is nearly killed. The Sparticles chase the digger down the road but it gets stuck and Reese drops the Decoder. The digger destroys the Decoder and Rocky drops the bucket and lets Reese out. Before they leave, Reese reveals that before it was destroyed, she saw the message decoded. They leave, and Rocky's brother finds a note stating that he has stowed away with the Sparticles to get their mum back.
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?
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 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.
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.
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. The Sparticles get the treasures back and are going to try to find the Stone of Artos.
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.
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.
In a world with no adults, now ruled by teenagers and the monstrous Queen Kylie, the Sparticles join the fight for survival.
The Sparticles' mission to send Queen Kylie and the Teen Parents back to the dimension they came from hits a snag. Former Emperor Fizzy is after them.
The Sparticles find a third person with 'powers' like Reese, and the mission to rid the world of Queen Kylie moves up a step with the discovery of a curious map.
Reese uses her 'powers' and the help of Holodora to work out the secret to ridding the world of Queen Kylie and the Teen Parents.
Ernesto stages a rebel rescue mission to spring Orion from Kylie's citadel, and learns how he nearly got named something far less revolutionary at birth.
Frankie's hunt for her lost rabbit discovers the spooky forest-dwellers, a new sensitive and a case of identity theft by a 'friend' of Queen Kylie.
Reese and Aris have a close encounter with the missing adults, and Holly's mystery illness is diagnosed by a new sensitive with special healing powers.
Queen Boudicca's daughter wants to help the Sparticles fight against Queen Kylie but she urgently needs to return to her own dimension to fight the Romans.
Ernesto and Serena stage a daring raid on Kylie's Citadel, where Dora's discoveries have assisted Queen Kylie in her plans for world domination.
In a haunted house where a ghost buster is busy disproving the existence of a ghost, why are the Sparticles disappearing one by one?
Both Queen Kylie and the Sparticles are held up in the race to the circle of perpetual time by troll queen Trina. Do trolls really eat people?
The Sparticles discover the oldest man in the world in his circular garden. Is he the last clue for them to rid the world of Queen Kylie?
The comet approaches, and time is running out in the hunt for the seventh sensitive to help rid the world of Queen Kylie.
