The story picks up one year after the attack on Xavier Institute that caused the disbanding of X-Men and the mysterious disappearance of Professor X and Jean Grey. Wolverine must reunite his team to find out what happened that fateful night. Their position as mutants doesn't make things any easier as the MRD (Mutant Response Division) is hunting down and exterminating them.
The pilot episode of the Wolverine and the X-Men series show Logan leaving the X-Men, leaving Rogue and Hank utterly sad about his departure. Meanwhile, Charlie, Kurt, and the X-Men in the lab are succumbed to a bomb blast, leaving them unaccounted for. A year later, when the Mutant Response Division (MRD) targets innocent families, Wolverine decides to bring back the X-Men together.
The Brotherhood has attacked the city and issued a warning to Senator Kelly. The X-Men are desperately trying to stage a comeback when Domino convinces Rogue to join the Brotherhood and protect their unique abilities. Before the Mutant Registration Act is passed, Rogue uses her abilities to find out the Senator's itinerary. Will Rogue betray the X-Men for her selfish needs?
With Rogue having abandoned the X-Men, they are left with no choice but to continue on the mission to bring back the X-Men together. Logan is approached by Emma Frost, the greatest telepath to join the X-Men under the condition that she reveals the location of the missing Prof. Xavier in Genosha, and in return, she obtains access to the cerebrum. But they must endure Magneto to reach Charles.
Charles tries to telepathically communicate from the future, warning the X-Men about the damage Storm has brought to Africa. The X-Men are surprised to have found that Storm would do that to her own home. They race to Africa in order to prevent the damage before it happens. However, they realize they're too late as Storm's mind has been invaded by an evil, powerful telepath, her former employer.
The M.R.D wants to portray mutants as a potential danger to the humans and takes necessary steps to fulfill it. The Magma out of fear starts turning into a burning lava and causes mayhem. An ability-inhibitor collar built by Forge which helps to control mutant abilities is stolen by Gambit for Dr Sybil Zane who in turn works for Senator Kelly and now it is up to Wolverine to get it back.
Nightcrawler spies on the ship that is transporting mutants to Genosha. Pirates attack and capture few powerful mutants along with Nightcrawler while the rest of the mutants are left deserted in the wrecked ship. The pirates are looking for fighters within the pool of high-level mutants attacks the ship. Nightcrawler alone defeats the pirates and rescues the mutants.
S.H.I.E.L.D agent Nick Fury opts for Wolverine's help to defeat Hulk by intimidating him and falsely accusing Hulk of terrorising the Canadian Rockies. The real monsters terrorising the Canadian Rockies were the Wendigo. Wolverine and Hulk team up to fight against the monsters.
Nitro is a self-detonating mutant and is abducted by the Brotherhood to detonate him in Genosha. Professor Charles Xavier informs Wolverine of the consequences that will drastically change the future of the mutant race. The X-Men tries to rescue Nitro from the Brotherhood but the Brotherhood gives a tough fight back to the X-Men It's up to Wolverine and the X-Men to secure the mutant's future now
The Sentinels capture Professor Xavier and they steal the Cerebro from him. Later, he is transferred to a prison where he teams up with Bishop and other prisoners to break free from there, but they must fight an army of Sentinels. In the present, Wolverine and the other X-Men visit the old laboratory of Bolivar Trask to gather more information about their new clue, the Master Mold.
Nightcrawler travels to Genosha, Magneto's promised land for all the mutants. Accompanied by Scarlet Witch, his tour guide, provided by Magneto, Nightcrawler gets a full access tour of Genosha. But soon he discovers that Genosha is just a prison facility for those who choose to disobey Magneto's command. Will he reveal Magneto's plan to the X-Men before Magneto captures him?
Wolverine with the help of Emma Frost tries to uncover his forgotten past. He learns about Christopher Nord, whom he was supposed to assassinate but failed. Bolivar Trask, the man responsible for Wolverine's messed-up past, is now after Nord's daughter Kristie, who has the same powers like her father. Will Wolverine be successful in protecting her from Trask?
After learning that Mr Sinister has Jean Grey, Cyclops, tries to track down Mr Sinister all by himself. He invades Sinister's lab and forces Arclight to give away the location of Sinister's hideout. But, to Cyclops's surprise, Mr Sinister was not the one who kidnapped Jean, but he simply wanted to avenge the loss that Cyclops has brought upon him and his team. Will the X-Men rescue Cyclops?
Rogue discovers that the Brotherhood is working with Magneto to attack the X-men, but nobody trusts her. Soon the Brotherhood launches an attack on them but the X-Men successfully defend themselves. Following the recent attacks on MRD, the X-Men soon discover that the attack on them was just a distraction. To stop a war, the X-Men must stop Magneto from using Tildie Soames as a weapon.
When Wolverine gets the news that the Weapon X team is after Maverick's daughter, Kristie, to turn her into a mutant weapon, he is set on a journey to rescue her. In the process, Wolverine and Mystique face their old WeaponX teammates, Sabretooth and Maverick. Will Wolverine be successful in saving Kristie or will Kristie have the same fate as Wolverine in the hands of Professor Thorton?
Nightcrawler and Scarlet Witch are abducted from Magneto's facility at Genosha by a mutant named Mojo, who wants them to fight against his goons for his own entertainment. Nightcrawler decides to avoid fighting and runs, but he gets shocked when he discovers that their next opponent is none other but a ferocious Wolverine who is under Mojo's control.
While gathering information about Trask's research facility, the X-Men stumbles across a massive Sentinel production facility. Wolverine gets captured and his powers are studied by Trask. In future, Trask's studies about Wolverine's powers help them create a new Sentinel. Professor Xavier from the future sends a message to Wolverine and warns him about the dangers Trask's research will cause them.
Wolverine visits the mansion and finds out that the X-Men have been abducted by ninjas. He understands it to be the deed of the Silver Samurai whom he had once defeated in order to win over his love, Mariko. Even though Wolverine had won the fight, Mariko had chosen the Samurai. Why then has the Samurai challenged Wolverine again?
The mutants discover what the Master Mold actually is. The MRD or the Mutant Response Division begin to project Wide Awake to detect and capture all the mutants of the world through an artificial intelligence that is controlling and operating the sentinels. Tricked by Master Mold, the X-men find themselves ambushed. Will they be saved or captured?
This time, Wolverine and the X-Men deals with the agony of Angel. Angel comes to know from Wolverine that his father is close to creating a cure for the mutants which will have the power to destroy the X-gene. Furious, Angel confronts his father who orders the MRD to take action. This results in Angel losing his wings and resorting to evil. Will he change for the worse?
The 'Breakdown' reveals the actual reason for the explosion after which Charles and Jean had disappeared in the first episode. In the present, Cyclops is haunted by the memories of Jean which makes him lose a battle with Juggernaut allowing him to escape from the hold of the X-Men. As Emma helps Cyclops to erase memories of Jean we are shown some very important aspects of Cyclops past.
After a suspicion that Jean may be responsible for the explosion in Genosha, Professor X and a team of future X-Men try to uncover details about the explosion to prevent an apocalypse. The only way they can get exact information from Master Moul's detention centre which is guarded by reprogrammed sentinels. Will Marrow agree to sacrifice Rover to gain information or will they fail in their quest?
Senator Kelly sends Gambit to Genosha, Magneto's island, to steal his helmet and destroy his resources to get an upper hand on him before the impending war. Gambit charms Polaris, who tries to help him steal the helmet and destroy important places on the island. Before an infuriated Magneto goes to war, Wolverine intervenes and helps both of them gain an insight to the impending apocalypse.
Scott believes it was his fault that they lost Jean but she survives even though she has a memory loss. Jean is tracked down by Scott and Emma in a hospital before they are confronted by Archangel who takes them to Mr Sinister to extract their genetic codes to create a really powerful mutant after which they are to be killed. Will Archangel finally get rid of Jean and Scott?
Logan (Wolverine) rescues a child but one of the family members tries to turn him into the MRD as he is a mutant. He manages to escape but the MRD captures the family instead, as Logan is a wanted man. Logan decides to help the family as the MRD is a notorious organisation capturing mutants to misuse their powers for world domination. Will Logan be successful in his attempts to stop the MRD?
This episode focuses on Wolverine finally getting together the X-men who went their separate ways after the initial explosion at the Charles Xavier's School. Magneto rounds up his own army of metal Trask sentinels. Emma at long lasts discovers HellFire clubs' real intention on using the power of the phoenix through the single strongest telepath in the world of mutants, Jean Grey.
Scott learns the reason for Jean's Phoenix outburst earlier. Professor Charles and Logan take on the sentinels guarding Master Mold. Phoenix is trying to return to Jean and they can't control it. Jean takes on the extracted Phoenix rampaging the city. Lorna mistakenly unleashes the full potential of Master Mold. Will the x-men save the world from the Phoenix and prevent the rise of the Sentinels?