(As usual I moreso recommend people to simply read part I, and I doubt anyone is going to stumble into part 2 blindly.
But these summaries serve also a reminder rather than a warning or a recap for people with little time, so without further ado)
THE STORY SO FAR
One morning a young duelist arrives in a small town, with no memories of his former life or any idea of how he got there. All he has with him are two dueldisks, cards and a crystal attached to a necklace. All he remembers is a name that might not be his own; Uno. In the town he meets other duelists like the sisters Alice and Emily Brandt, and their neighbor Eric Stonewell. They want to genuinely help him recover his memories, but also come to find out that he possesses cards and powers they've never seen before; the performapals, odd-eyes dragon and the pendulum monsters. His power also draws the attention of Dreamworld, the current card supplier of this world. Its master sends two disciples to investigate; Zach Creffield and Iria Silver. At first they try to detain him for using cards that were not yet released on the market'. Eventually they clear him of charges, but they continuously keep an eye on him and his friends. They also tell him that their master already knows a man named Dom, and that Uno has to prove himself at an upcoming tournament before he can meet their master.
With this new information, Uno and his friends decide to enter the tournament. Along the way though they encounter the guilds; three separate clubs of duelists who each specialize in one brand of extra deck monsters. Cassius, a former friend of Emily and Alice, is the leader of the synchro guild and he welcomes them openly. But when Dreamworld releases information of pendulum monsters to the public, other guilds also begin to show interest in Uno. While Uno does not gain the favor of the XYZ-guild's leader and previous tournament champion; Adamant. He does defeat duelists from the synchro and fusion guild. Yet, with Alice's help, they manage to form their own independent guild for the tournament. Meanwhile Emily joins the synchro guild. Eric secretly enters the fusion guild as a spy for Dreamworld, to help them fight counterfeiters and mysterious duelists who might or might not be affiliated with one of the guilds. One such duelist, June, attacks the synchro guild with fusion monsters. A synchro duelist, August, also attacks Dreamworld and its master, Dom. In both cases the attackers are driven off and escape miraculously.
Ultimately, the tournament begins. Zach gets beaten in round one by the leader of the Fusion Guild, Dame Phoebe. Emily, Eric, Alice all make it to the next round with their guild-enhanced decks. Uno also makes it to round two, and after he defeats Iria Silver herself, he earns himself a meeting with Master Dom. But he does not know who Uno is. Only that he and UNO are not the same man, and that UNO is the true creator of the dueling game; the writer of the stories that the cards were drawn from. In the mean time, Emily is eliminated by Eric. And Cassius is thrown out of the tournament due to an accident with no known causes. Then, in the third round, Uno encounters the third member of the unaffiliated duelists; January. He reveals that he possesses a crystal like Uno; called a pendulum. After a fierce duel, which drives Uno berserk and pits him up against the tournament host Dom himself, he is pushed through dimensions and sent into another world by his own pendulum. A world that he realizes is his true home, another timeline that exists alongside the first.
Before he manages to return to his friends, Alice faces Adamant in the fourth round of the tournament. Despite all odds, Alice manages to come out on top and bests the former champion. Unfortunately this drives the XYZ-guild to break the rules and take over the tournament with all their duelists. The XYZ-guild wants to break into the digitial vaults of Dreamworld, where Dom has hidden data of the most powerful cards. But Dom preemptively encrypted the data and hid the decryption key card in three cards; fusion, synchro and xyz dragon counterparts to Uno's Odd-Eyes dragon. The disciples, Uno and friends manage to sneak out of the tournament with the three cards. However Eric betrays everyone and steals the fusion dragon to give it to Dame Phoebe. It is now that the unaffiliated duelists return with their leader; December. Together they end the fights at the tournament, get the information they want from Dom and almost take Uno away for being a pendulum user and a timetraveler like them. Uno's friends step in and temporarily they push the four duelists back.
Throughout these adventures, Uno ran into three strange entities; the sisters of Prophecy. Cloe, Veronica and Margot. They answer three questions each time, seemingly knowing all about the past, present and future. They also help him develop his powers of the pendulum and of the dragons. Making him realize that the cards possess a spirit too. They were once alive, and there were worlds before the current one.. in which they lived.
Adamant, desperate to regain power in his own guild, leads an attack on Dreamworld where the two remaining cards are now. Cassius defeats Adamant with his new synchro dragon, and captures him. Everyone relocates to the synchro guilds headquarters. Zach and Uno secure a virtual meeting with the real UNO to acquire a card printer, which will let them create new pendulum cards. The duelists also get Eric back on their side, who turns out to have been brainwashed by Martel, a secret member of the fusion guild. In the mean time a captive Adamant reveals his motives to Alice, the only duelist he can respect. The XYZ-guild feared an invasion from the other world they had already discovered, and he believed one of the other guilds was allied with that world. In the end Adamant abandons his guild to join Uno. The former second in command, Ichirou, takes over and steals the XYZ-dragon from Uno.
That guild turns out be to the synchro guild. Cassius and several other duelists form their own secret organization; The Circle. Their founder, Vesper, discovered a way to link one mind with the mind of its alternate self in the other timeline. Through linking minds, The Circle has infiltrated both worlds. Their eventual goal is to synchronize all minds of all counterparts, to avoid the great disaster. They believe that one timeline will inevitably be destroyed by the other, and this is the only way they can save as many people as possible. Before they can bring Uno and friends into this, Doms quick thinking gets them out and they manage to alert the guilds to the presence of The Circle. Emily is forced to stay behind to keep Cassius from pursuing them, and she is captured after Cassius defeats her. But the Fusion and XYZ-guild soon overwhelm the synchro guild. Cassius, Dame Phoebe and Ichirou duel for the rights of the Fusion, Synchro and XYZ Dragons. Dame Phoebe ultimately wins the threeway duel and claims all dragon cards for herself, thus absorbing both Dreamworld and all other guilds into the fusion guild.
Uno and his friends barely manage to get away. Zach was taken down by Martel, Dom was banished to the other world by Vesper. Through other revelations, they come to find out that not only was Alice adopted into the Brandt family, but she was also a timetraveler like Uno. She accidentally fell into the current world after her previous world was destroyed by the guardians of time; the spirits who clean up dimensions that cease to exist after its pendulums abandon it. Now back where he started, Uno is confronted again by December and the other Calendar duelists. They want both him and Alice to disconnect from the present world, where they should not exist. But Uno refuses and duels December once more. He learns that December and the others lost their worlds too, to the original timetraveler...Tempus. And they have been chasing Tempus throughout timelines for an eternity. In the end, Uno is forced to draw with December. The resulting explosion scatters everyone and pushes Uno, Iria, Alice, Eric and Adamant into the other timeline; his homeworld. And that is where they are now..