Following the temporary retreat of the Altana Liberation Army from the Kabuki District, the state of the war has seemingly improved. However, as the Oniwaban, Shinsengumi, and residents of the district combat the army's remnants, Edo's greatest inventor Gengai Hiraga is abducted. Responsible for causing the enemy's withdrawal by rendering their weapons useless, Gengai's nanomachine virus is now at risk of being shut down. Meanwhile, a laser capable of obliterating a planet is activated in Earth's orbit on the Liberation Army's mother ship. Another battle ensues when Shinsuke Takasugi and the rest of the Kiheitai arrive on the vessel to stop the weapon from firing. Forced to fight a war on two fronts, the Yorozuya and their allies must prevail on both sides to save Edo and the rest of the world.

After the fierce battle on Rakuyou, the untold past and true goal of the immortal Naraku leader, Utsuro, are finally revealed. By corrupting the Altana reserves of several planets, Utsuro has successfully triggered the intervention of the Tendoshuu’s greatest enemy: the Altana Liberation Army. With Earth as the main battleground in this interplanetary war, Utsuro's master plan to destroy the planet—and himself—is nearly complete. An attack on the O-Edo Central Terminal marks the beginning of the final battle to take back the land of the samurai. With the Yorozuya nowhere in sight, the bakufu all but collapsed, and the Shogun missing, the people are left completely helpless as the Liberation Army begins pillaging Edo in the name of freeing them from the Tendoshuu's rule. Caught in the crossfire between two equally imposing forces, can Gintoki, Kagura, Shinpachi, and the former students of Shouyou Yoshida put aside their differences and unite their allies to protect what they hold dear?

Gintoki, Shinpachi, and Kagura return as the fun-loving but broke members of the Yorozuya team! Living in an alternate-reality Edo, where swords are prohibited and alien overlords have conquered Japan, they try to thrive on doing whatever work they can get their hands on. However, Shinpachi and Kagura still haven't been paid... Does Gin-chan really spend all that cash playing pachinko? Meanwhile, when Gintoki drunkenly staggers home one night, an alien spaceship crashes nearby. A fatally injured crew member emerges from the ship and gives Gintoki a strange, clock-shaped device, warning him that it is incredibly powerful and must be safeguarded. Mistaking it for his alarm clock, Gintoki proceeds to smash the device the next morning and suddenly discovers that the world outside his apartment has come to a standstill. With Kagura and Shinpachi at his side, he sets off to get the device fixed; though, as usual, nothing is ever that simple for the Yorozuya team. Filled with tongue-in-cheek humor and moments of heartfelt emotion, Gintama's fourth season finds Gintoki and his friends facing both their most hilarious misadventures and most dangerous crises yet.

After joining the resistance against the bakufu, Gintoki and the gang are in hiding, along with Katsura and his Joui rebels. The Yorozuya is soon approached by Nobume Imai and two members of the Kiheitai, who explain that the Harusame pirates have turned against 7th Division Captain Kamui and their former ally Takasugi. The Kiheitai present Gintoki with a job: find Takasugi, who has been missing since his ship was ambushed in a Harusame raid. Nobume also makes a stunning revelation regarding the Tendoushuu, a secret organization pulling the strings of numerous factions, and their leader Utsuro, the shadowy figure with an uncanny resemblance to Gintoki's former teacher. Hitching a ride on Sakamoto's space ship, the Yorozuya and Katsura set out for Rakuyou, Kagura's home planet, where the various factions have gathered and tensions are brewing. Long-held grudges, political infighting, and the Tendoushuu's sinister overarching plan finally culminate into a massive, decisive battle on Rakuyou.