Okay, keep in mind that I'm currently at Episode 105 as I write this (Ep 105 marks the end of the "Shinsengumi Rebellion" story arc). This is, in my opinion, the ideal way that Gintama should conclude. Though I personally hope it'll be one of those anime series that will never seem to end, like One Piece. I guess this can be considered fan fiction, and I by no means wish to offend the author of Gintama, this is just my answer to "What do you think would be the best way to end Gintama?" Read it or don't. :)
--> Another Joui War should take place, in which most of the Joui factions finally team up to rid Edo of the Amanto government. However, the Joui faction known as Kiheitai (led by the series main antagonist, Takasugi Shinsuke) would perfer that Edo be destroyed entirely so that civilization in Edo can start again from scratch, led by Samurai rule. All three groups are at war with each other, which causes great mayhem and chaos across Edo.
--> The Shinsengumi and other government protection groups are unable to contain the chaos, due to the Kiheitai's use of 'living' cyber swords such as Benizakura (refer to Episode 60?), and the Joui's massive amount of members and their pirated technology from other planets. This period of endless voilence causes the sensei of the disbanded Jouishishi group (one of the original Joui factions) to return to Edo, who had since been living as a hermit in the countryside ever since the failure of the Joui War. This is the sensei who actually appears in the anime as Gintoki/Katsura/Takasugi's teacher when they were children.
--> This sensei, now aware that his disciple Takasugi is running rampant with an extremist view, vows to stop Takasugi and summons his other Jouishishi disciples to Edo (the children seen alongside Gintoki/Katsura/Takasugi that he teaches - refer to the ending animation of Episode 104). Gintoki rejoins this revived Jouishishi, along with Sinpachi and Kagura. Thus, the Yurozuya have taken up their last freelance job; to merge into the Jouishishi group and free Edo whilst stopping Takasugi. Eventually, Katsura also rejoins this new Joushishi, and allows the Jouishishi group to effectively control the Joui as their army.
--> The Kihetai and Jouishishi/Joui finally confront each other in an epic battle above Edo Tower. The Amanto government see this as a great opportuntiy to mess with the underground reactor beneath Edo Tower which will explode and destroy all of Edo (refer to Episode 71, I think) and the gathered armies above. As such, all the Amanto evacuate the city and plan to a rebuild Joui-less Edo when its destrustruction comes. However, they leave all the humans behind, and so the Shinsengumi take it upon themselves to evacuate all the innocent human bystanders out of Edo. However, they discover that the border of Edo has completely been blockaded by an army of Amanto - and so the Shinsengumi have an epic battle with them whilst the people they saved can escape.
--> In the Battle of Edo Tower, sensei is killed by Kihetai (maybe in a Obi-Wan Kenobi kind of death? refer to Star Wars Episode IV, lol), which sends Gintoki and Katsura into a rage and both fight Takasugi together. After a long battle, an airship carrying some of the fighting Jouishishi members crashes into Edo Tower. They survive, but find themselves inside the tower, where an alarm informs them of the inevitable self-destruction of Edo. They rush down the tower in hopes to find underground access to stop the explosion. In case they don't succeed, they radio the Joui and inform them off the newfound situation.
--> Learning of the upcoming doom, the Joui retreat from the skies of Edo and fly off, but the Kihetai follow in hot pursuit. After a long battle, Gintoki and Katsura both fight alongside each over to finally defeat Takasugi. Takasugi, now defeated, feels too disgraced that his ultimate goal of destroying Edo has been fulfilled by the enemy Amanto and not by himself. Wounded and frustrated, he jumps from the side of the airship just as the reactor explodes. The Joui members that tried to stop it have failed and have been the first to die from the explosion. Takasugi, whilst in freefall above Edo, watches the explosion as it comes at him. Before he is engulfed in the explosion as he reaches the ground, he sincerly wishes Gintoki and Katsura good luck in rebuilding Edo (they are his former friends, comrades and classmates, afterall).
--> Flashforward to two years after this new Joui War. The war ended the same moment Edo was destroyed. Now the Joui have instigated a new government, which is largely human but still contains an Amanto ambassador for a hopeful peaceful future. This ambassador is Kagura, and Shinipachi is a high-ranking offical now within this new governemt. The Shinsengumi loyally protect this government and all of Edo from any more aggressive Amanto invasions. The unified Joui factions, still under Katsura's command, head into space to free other repressed planets from the Amanto. It's also revealed that Elizabeth is a Jouishishi member who is thought to died during the original Joui War - Elizabeth was saved by Katsura at a young age and Elizabeth has admired him and wanted to repay the debt ever since, but his love for an Amanto woman made him leave during the Joui War and don his current look. Now his debt has been fulfilled, Elizabeth decides to stay in Edo and make a new Joushishi of new young disciples. Of course, we never see Elizabeth's real face or learn his real name. Ever.
--> Gintoki calls himself Shiroyashi (White Dragon - his nickname during the original Joui War) once more and sets off to other regions of Japan to free them of their Amanto-repressing governments once more, all which are far more agressive regimes than that seen in Edo. Shinpachi and Kagura say their goodbyes to him, and Kagura allows Sadaharu to go with Gintoki in his mission. He rides off into the sunset riding Sadaharu and looks back at Edo - which is starting to build a new Edo Tower, in the shape of a giant sword, at the heart of the city, which has plaques on the ground level which show the names of those who died, especially the Joui members. And below all the names is etched a message on the Edo Tower wall - the message which Shinpachi says at the beginning of the episodes back in Season 1 (ya know, the "Land of the Samurai" speech) but changed to show that the Era of the Samurai has rebegun.
--> It should also be implied that, just before the end the original Joui War, Sensei stole Amanto nanotechnology - specially, experimental nanomachines which would work inside the user's body and repair/regenerate the user's body when they are injured. However, Sensei was unsure about the use of thise technology on his disciples, but Gintoki knew that they needed it's help if they were to win the Joui War, and thus Gintoki volunteered to be injected with the nanomachines. Gintoki's body accepted the nanomachines and there were no bad-side effects; except that the nanomachines now within his body quickly drained his body's store of sugar. This is why Gintoki is always seen as crazing sugar and sweets during the series, whether he is aware of the reason or not. The nanomachines were then to be used in the other Jouishishi members, but the Joui War ended before it was neccassary. Gintoki is now pratically invincible because of his nanomachines. This explains how he survived his fatal wounds in Episodes 107/108, and is never seen with scars on his body. However, in exchange for this invincibility, Gintoki's life expectancy is much shorter than the regular person, and so he will probably die during his new crusade that he started as the new Shiroyashi. Thus, he dies fighting and protecting people, which is the probably the best way for his character to end. And perhaps Gintoki suspects his impending doom, which is why throughout his life he protects others and spreads ideals of living peaceful and equal lives (similar to the 'Love and Peace' message Vash from Trigun spreads around the world).
Woah that was much longer than I thought. And I forgot to include Kagura's father and brother. Oh well, I'm sure the author of Gintama will resolve those eventually lol. Hoped you found my ideal ending to be a good read, or found it interesting at least. ^_^
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