Despite the destruction of the mechanization home world Andromeda, the machine empire is still swept across the galaxy and Earth has become a battleground. Having returned from his journey aboard the train Galaxy Express 999, Tetsurou Hoshino joins the resistance and fights alongside others who have retained their humanity. When the 999 returns to Earth, Tetsurou receives an enigmatic recorded message from his former traveling companion Maetel, telling him to board the train once more. Fighting his way to Megalopolis station, he makes it onto the train just as it departs. This time, however, Tetsurou is met with several mysteries: Maetel is nowhere to be seen, an ominous "Ghost Train" has appeared, and the ultimate destination of the 999 is unknown. Amid all this, Tetsurou finds himself confronted by the mysterious black knight Faust and soon discovers the machine empire's darkest secret.

Nobita and his friends embark on a quest to find an ideal land called Paradapia, similar to Thomas More's Utopia. Guided by Doraemon's futuristic gadgets and time-travel abilities, they uncover Paradapia's secrets and face challenges, including encounters with a bounty hunter named Marimba. The story revolves around their efforts to unravel the mysteries surrounding Paradapia, leading to a positive resolution and the anticipation of future adventures.

Forced to abandon their home planet of Cybertron due to the threat of the Blackhole, Optimus Prime prepares to lead his autobot warriors to Earth. Just as they are leaving they are confronted by Vector Prime who warns Optimus Prime of the threat to the galaxy if the four Cyber Planet Keys are not gathered in time. However, Megatron has plans of his own for the universe. As they embark on the search, they land on new planets which are inhabited by different Transformer races as well as the Convoys who lead these planets.

Nihility is the world's greatest catastrophe. Humans can only unite their allies against "blessers", monsters from the world of nihility. Shazhou, the continental border, becomes an important line of defense against invaders. A dark force called "Shadow of Blessing" is looking for the power that has been sealed. Dark Island, the leading state of the human alliance, sends White Wolf Yujia to destroy the dark force. But a mysterious girl called Coral from the world of nihility causes a storm in Shazhou. The red thread of fate connects everyone holding the belief of uncovering the historical truth hidden in nihility. The girl is fighting against her fate beyond her belief, and a romantic legend officially begins.