1. Benizakura Arc
Episodes: 58 to 61
Benizakura arc is probably the first serious arc in the series. Gintoki Sakata, and his friends, Kagura and Shinpachi Shimura, become involved in a plot involving Benizakura sword, which is said to be cursed. Elizabeth requests Yorozuya to find Katsura who went missing. As the investigation began, both the cases seem to have a relation to each other.
The arc features several major characters from the series, including Takasugi Shinsuke, a former comrade of Gintoki and Katsura, and his group, the Joi Faction, who are seeking to steal the Benizakura sword to further their own goals.
It showed how serious and bloody the series can be and also the intrigue behind Gintoki and Takasugi.
2. Yagyu Arc
Episodes: 76 to 81
This is a more light hearted serious arc that introduces Kyuubei, one of the most important characters in the series.
The Shinsengumi asks Otae for help when an arranged marriage is set up for Kondo with a gorilla. However, an old friend of Otae named Kyuubei comes back and claims that Otae promised to marry him in their childhood. As a result, the Yorozuya and Shinsengumi team up to go to the Yagyu house to retrieve Otae, leading to a conflict between the Yagyu family and the Yorozuya-Shinsengumi alliance.
3. Okita Mitsuba Arc
Episodes: 86 to 87
Okita Mitsuba arc is a significant part of the series, as it focuses on one of the main characters, Okita Sougo, and his relationship with his elder sister, Okita Mitsuba. This arc is definitely the saddest arc by then.
Okita’s sister, Mitsuba, comes to the Shinsengumi to announce her upcoming marriage. However, it is revealed that the man she is marrying is an evil person who only wants to use the Shinsengumi’s support. It is also revealed that Hijikata has a past with Mitsuba. As Mitsuba’s terminal pulmonary disease progresses, she tells Sougo how proud she is of him before she passes away.
4. Shinsengumi Crisis Arc
Episodes: 101 to 105
Hijikata obtains a cursed sword that causes him to act strangely and puts his position in the Shinsengumi at risk. Itou Kamotarou, an adviser to the Shinsengumi, returns to try to improve the group. However, Hijikata realizes that there is a conspiracy to remove him from power and dismantle the group, and he asks Gintoki for help in uncovering and stopping this plot.
5. Yoshiwara in Flames Arc
Episodes: 139 to 146
This can be considered a game changing arc in the series. It introduced Tsukuyo and also Kamui, two of the most important characters in the series. Also the worldbuilding greatly improved in this arc.
A young pickpocket named Seita accidentally runs into Gintoki, and the Yorozuya decide to help Seita in his quest to save enough money to visit his mother in Yoshiwara. As they journey to Yoshiwara, it is revealed that the town is controlled by a Yato named Housen, and Kagura’s brother Kamui becomes involved. In order to rescue Seita’s mother, Gintoki and the Yorozuya must confront Tsukuyo, a member of the Joi Faction.
6. Red Spider Arc
Episodes: 177 to 181
A mysterious man with a tattoo of a spider on his neck arrives with the intention of orchestrating a terrorist attack on the Edo Tower and bringing down Yoshiwara. In an attempt to gather information about the man, Gintoki and Tsukuyo infiltrate the Benigumoto, a group known as the Red Spiders. However, they are quickly discovered and surrounded. Despite the danger, they manage to escape on their own, but the mystery man reappears and is revealed to be Jiraia, someone Tsukuyo seems to have a past with.
The chemistry between Gintoki and Tsukuyo was great in this arc and this arc showed the vulnerable side of Tsukuyo.
7. Kabukicho Four Devas Arc
Episodes: 210 to 214
A girl named Pirako Chin, comes to the town of Kabukicho looking for the strongest person in the area and is told that it is Gintoki. When the Yorozuya learn that Pirako is a violent gangster who wants to help Gintoki take control of the Kabuki District, they are hesitant to accept her into their group. This leads to a conflict between the four factions in the town.
The first arc where it felt Gintoki actually lost his mind for a moment. Gintoki vs Jirocho is an iconic moment in the series.
8. Thorny Arc
Episodes: 244 to 247
Sasaki family is a highly prestigious family and Tetsunosuke is a member. Tetsunosuke has joined the Shinsengumi, but he actually prefers the elite Mimawarigumi police squad. He was assigned to the Shinsengumi because he was considered a troublemaker. Kondo assigns Tetsunosuke to work as an assistant for Hijikata, and Hijikata must endure Tetsunosuke’s quirks.
9. Courtesan of a Nation Arc
Episodes: 257 to 261
Gintoki goes to Yoshiwara to meet the most famous courtesan in the area, but discovers that she is actually an old woman. This event sets off a series of events that leads Gintoki and others to confront Tokugawa Sada Sada, the former Shogun and the most powerful man in the country.
10. Beam Sword Style Arc
Episodes: 262 to 264
Otae decides to reopen the family dojo that her father had abandoned. She meets a former instructor who had disappeared under mysterious circumstances and agrees to help her. However, the instructor is enigmatic and is hiding a secret that has the potential to destroy the world.
11. Shinigami Arc
Episodes: 279 to 281
A serial killer is targeting drunkards on the streets and Gintoki encounters a Shinigami who asks him to help it commit suicide. However, Gintoki renders the Shinigami unconscious and brings it back to his home, where it is revealed that the Shinigami is actually a young woman named Ikeda Asaemon. As the story progresses, it becomes clear that Gintoki has deeper connections to these events than originally thought.
12. Shogun Assassination Arc
Episodes: 300 to 307
Nobu Nobu and his allies in the Kiheitai and Harusame are plotting to assassinate Shige Shige. Matsudaira comes up with a plan to secretly transport Shige Shige to Kyou with the help of the Oniwabanshuu, Shinsengumi, and Yorozuya in order to protect him. To save the Shogun, they must confront rival ninja, a highly formidable terrorist organization, and Yato, one of the strongest Amanto races.
Additionally, the long-awaited battle between Gintoki and Takasugi takes place during this arc. This is considered to the best arc in the series and rightly so. From the start to the end, it was perfect.
13. Farewell, Shinsengumi Arc
Episodes: 308 to 316
Following the funeral of Shige Shige, Nobu Nobu continues to increase his power and influence after serving as Shogun for three months. He starts by capturing Matsudaira and Kondou and announcing their execution for failing to save the Shogun. The Shinsengumi is also dissolved for the same reason. In order to prevent the deaths of Kondou, Matsudaira, and Katsura, who is later captured, Hijikata, Okita, and the other officers join forces with the Joui group and the Yorozuya. The Naraku and Mimawarigumi serve as the opposing forces.
14. Rakuyou Decisive Battle Arc
Episodes: 317 to 328
after the Shinsengumi leave Edo, the Yorozuya and Katsura’s Jouishishi group have been in hiding for several weeks. In response to a request from Imai Nobume, the two factions join forces to rescue Kamui and Takasugi from Utsuro and the Harusame. They also team up with the remaining Kiheitai and Sakamoto and his Kaientai. When Utsuro also targets Umibouzu, who is also pursuing Kamui, the situation becomes more complicated. All of these groups come together and engage in battle on the Rakuyou.
15. Silver Soul Arc
Episodes: 342 to 369 + Movie
Utsuro’s ultimate goal is to trigger a world war that will ultimately destroy Earth and himself, as well as the rest of the universe. In order to stop Utsuro, Gintoki and others must join forces with both old allies and adversaries to fight against the immortal and the victims of his scheme – a large group of furious Amanto who may no longer be receptive to reason.