Foreword: I've had several people ask me to write a summary of what would have happened had I continued the story. That much at least I can do. If you're clinging to hope that I might change my mind and continue this some day, and don't want the story to be spoiled, please don't read any further.
Be warned, I'm not going to bother even proofreading it, so you'll see how many mistakes my stories would have if I didn't. (Hint: a lot.)
Immediately upon leaving the Sabaody Archipelago, Naruto and his crew are sent to answer a call for help from an island nation shortly into the New World. It is home to the Hyuga, a human like race with eyes that function pretty much like the Byakugan from canon. Although the Juken is more about pressure points than chakra points, as the one piece world doesn't really have chakra.
Upon arriving on the island, Naruto is chased off by the Hyuga, with them claiming he's the one who's been attacking them. This is later discovered to be the work of Gekko Moria. Back when he was still one of the Shichibukai, he used his influence to have Naruto's corpse (remember when he died?) delivered to him.
Later, when Rob Lucci had been recovering from his loss to Luffy, Moria had tracked him down and stolen his shadow, which he had placed in Naruto's corpse. He had been using Naruto's corpse to abduct any Hyuga he could catch alone, killing some and stealing the shadows of others, creating his own undead Hyuga army. Naruto and his crew end up fighting, and eventually winning a battle against Moria, zombi Rob, and all the undead Hyuga he'd been able to gather so far.
Some takeaways from the fight are that Naruto sees the Rokuogun used enough that he's later able to work out how to do it himself. Also, they discover Haku is somewhat skilled in medicine and knowledgeable in pressure points when she is able to give him back use of his arm that he'd temporarily lost when being chased off upon their arrival.
Long story short, a big battle against Vegapunk's army of cyborg animals, his personal supply of Pacifista, and one prototype Mark II Pacifista. During the time it's confirmed by Vegapunk that he was responsible for Minato's death. He rues the fact that Minato had destroyed the android his village had been guarding before dying from his wounds and most of the parts were too damaged to salvage.
It had taken him years, and he still hadn't been able to reproduce a machine that could fight as well as the original. The one thing he had come away with was the AI unit, which he had modified to control all the Pacifista remotely.
During the battle, his lab is destroyed, although since Vegapunk only spoke through a monitor they don't know whether or not he was ever in there. But the AI unit was destroyed which renders the entire Pacifista line inoperable, something that infuriates the leaders of the World Government.
Jiraiya leaves the marines and goes into hiding, but Sarutobi turns himself in. He insists he manipulated the villages into joining the attack via superstition and talk of curses and he was the only responsible for the attack. They agree give the other villagers amnesty, but one of them remembers that Naruto was from their village.
Calling into question the loyalty of someone from the village of traitors, they decide to test him by having him take Sarutobi to Impel Down after the Hyuga Arc finishes. Naruto doesn't know that's what he's doing until he arrives at where Sarutobi is being held.
Naruto was going to refuse his order and help him escape instead, but Sarutobi insists he's going to turn himself in whether Naruto takes him or not for the sake of the villagers. He gives him a speech about having to decide for himself whether to abandon the marines or not, but not to make his decision rashly. Naruto eventually gives in and follows his orders, escorting Sarutobi to where he's imprisoned in Impel Down.
Dragon also shows up during this part of the story and tries to personally convince Naruto to join the revolutionaries. As angry as Naruto is at the World Government, he still refuses, insisting it's better to change the system from the inside than to start a war that will result in countless deaths.
Fire Country Arc:
The arc starts with Danzo, one of the leaders of the World Government, in a discussion with Tsunade, the elected leader of the Fire Country. The Fire Country is one of the most powerful nations in the World Government. It's also rich in Seastone deposits.
Because of this resource, they built shipyards in the country that build most of the marines' coated ships. With the loss of the so many ships in the Whitebeard War, as well as the destruction of those they had watching the other Yonko, they have a shortage of warships. So Danzo is demanding they increase the quotas significantly for the year.
Tsunade refuses as the World Government doesn't pay enough for the ships they do build. The shipwrights make most of their money building private ships once the quotas are filled for the year. They're already having trouble keeping their skilled craftsmen who could earn more in places like Water 7, and she fears raising the quote will cause many to quit.
She insists that if they want more ships they have to pay more for each one. The World Government is opposed to this, however, as they're afraid any increase in taxes would cause more nations to join Dragon's rebels. Danzo tries to talk her into some sort of compromise to which Tsunade agrees.
She tells him that rather than the 100 extra ships he wants he'll get 1. When he protests she insists he leave before she decides that 1 ship will be a life boat.
At this point Naruto finally reports to the marines that his mother is Kushina. This turns out to be bigger news than he anticipated, as Kushina is a direct descendant of the royal line of Fire Country, a fact the World Government is well aware of.
After the Void Century, the World Government was extending its rule over the entire world by force. When they set their eyes on the Fire Country, it became clear to the royal family that they couldn't win. Unwilling to sacrifice their subjects in the futile war, but not willing to bend the knee themselves, the sailed off with a few of their most loyal subjects, ordering those they left behind to surrender.
Their deeds and the promise to one day return had become an enduring legend in the Fire Country, and a favorite story of children throughout. This was actually how Nawaki has found his way to the Kushina. When he was younger he set out determined to find the royal family, a mission he succeeded at, even if she had no desire to go back with him.
The World Government had kept a close eye on their descendants throughout the centuries, given their ties to one of their most important member countries. At first as they acted as early rebels, attacking World Government resources and trying to stir up discord.
After enough generations their actions devolved into simple piracy. This is when the skull and crossbones was added to the flame that was the emblem of their country, leading to the birth of the original Burning Skull Pirates.
There were a number of generations that lived fairly normal and boring lives, but always some story an infamous grandparent would stir up a sense of adventure. So inevitably, the old pirate flag flew once again as they continued the family tradition.
Knowing of his lineage, Danzo hatches to plot to give the Fire Country the king they always wanted. With Naruto's loyalty to the marines, he would certainly approve an increase in the quota of warships that the military organization so desperately needed.
Avoiding Naruto becoming a political pawn like that was exactly why Minato had been so secretive about Naruto and his mother. Being the son of a pirate wouldn't be that big of a deal, but being the heir to a powerful nation was. It's also the reason Dragon was so interested in Naruto, and why Ivankov had left Haku to watch over him. It wasn't because Minato was his father, but because Kushina was his mother.
Speeding along, Tsunade hates the idea of someone who's never even set foot in Fire Country ruling over it, especially if he's just going to be a puppet of the World Government. But the citizens are wildly supportive of the return of the royal family.
Nevertheless, her words get to Naruto, and although he does agree to accept the crown, his first act is to give all authority to rule in his stead to Tsunade until such a time as he's fit to lead himself. To this end he leaves a clone with her to learn how to rule from her, attend public functions, and the like while he sails back off with his crew.
The Revolution Arc:
In this arc Kakashi reveals to Naruto that he was an agent of Dragon's since long before the story started. Guy had been his contact with Dragon's forces, although Lee somehow managed to remain unaware of Guy's connections to Dragon. He had actually been ordered by Dragon to ensure Luffy stayed alive, despite not knowing the relationship at the time.
He was, however, aware of Nojiko being Nami's sister. He believed that given the ties, even if Naruto ever defeated Luffy, at worst he would return the entire crew more or less unharmed to Kakashi, who could arrange for them to 'escape.'
As such, he'd been deliberately sending them on missions that would take them near where the Straw Hat Pirates had been reported. He could show the upper brass that he was making serious efforts to deal with Luffy, while following his orders from Dragon at the same time. This was also why Kakashi declared that it made sense when he found out that Luffy was Dragon's son, as he then understood why he'd been ordered to keep him alive.
Kakashi reveals all the dirty secrets of the World Government, with proof to back up many of his claims, such as those pertaining to previous usage of the Buster Call. It's Kakashi who finally convinces Naruto, and eventually the even more stubborn Tashigi to join Dragon's Revolution.
Shortly thereafter Dragon declares the formation of his own government with its own marine force. Nations and marine leadership split into sides. Dragon's marines are lead by Garp, Kakashi, Jiraiya, and of course Naruto. Kakashi had been holding back his true strength while he was an agent, wanting to keep his rank low enough that his work wouldn't be too closely scrutinized.
Jiraiya, on the other hand, had never made it past vice admiral solely because he'd already left the organization five times to pursue his true passion as a "writer." He was always pulled back when he was needed, but wasn't considered reliable enough to go beyond his rank despite his strength. Arrayed against them under the leadership of Kong are Sengoku and the three admirals.
Dragon also forms his own version of the Shichibukai. Those roles are filled by Luffy, Jinbei, and Boa Hancock at the least. I'm waffling a bit on whether to add in Ace and/or Kushina. Leaning yes on the former and no on the latter (her refusing the position of course.)
Even Luffy wouldn't accept the position easily, but I figured I could have Vivi, Nami, and some other finally convince him that all he had to do was promise not to attack anyone who didn't deserve it and then the "good marines" like Naruto and Garp wouldn't have to try to capture him. He could them pester Ace to join at least in name and help with the war.
Arrayed against them on the Shichibukai would be Mihawk and Doflamingo at the least, although I'm sure I would have written in some additions as well.
Basically the story would have ended with a big war the good guys eventually win, ending in the destruction of the World Government.
I had a vaguely planned arc involving Sasuke and Itachi. Sasuke wasn't out to kill his brother in this world. There was no murder of his clan, so he still idolized Itachi. He simply wanted to get out from his brothers shadow and make his own name to prove himself worthy of joining Itachi's crew (which had the fishman Kisame as the first mate.)
I know I wanted to maneuver into a fight with Naruto and Luffy vs Itachi, although not due to any real malice on Itachi's part. Itachi's devil fruit power would have given him the illusionary powers of the Sharingan. I had in my mind a scene where Luffy was hit with three consecutive Tsukuyomi attacks but still manage to drag himself back up and throw himself at Itachi again.
This fact would have impressed Naruto greatly, who had heard the details from Shino, who had been rendered unconscious by a single attack during an earlier meeting. It would also lead to a strategic withdrawal by Itachi, who had exhausted himself with the repeated use of the technique.
This would be done over the complaints of Kisame, who was confused as to why he even used that ability when he could have easily defeated his opponents with his bare hands. Not to mention how he could probably still take them in his weakened state even without Kisame's help.
I had planned an at least partial reconciliation between Naruto and Kushina, although I hadn't worked out the details. I did want to do a bit with Nami (having learned Naruto was royalty) trying to set up Nojiko with Naruto while Kushina did the same with Tenten.
Meanwhile I planned to have have Tashigi still going along with "pretending" to be Naruto's girlfriend. Despite being admonished by Nojiko repeatedly, she enjoys the dates and such they do for the public image so much that she continues to just pretend it isn't simply an act. She would do this for a while past the time skip.
The time skip was something I hadn't quite decided where to place. It would most likely have been either right before or right after the Fire Country Arc.
There you have it. If I'd actually written it, I would have fleshed out a lot, changed some ideas until they were nearly unrecognizable, and added plenty more. But this was my plan in its most current state (missing a few things I sure I forgot to include.)