The story went the same as the original timeline with Luffy following Ace everywhere regardless of all dangers and such. In the meantime, Leo calmly watched everything while practicing Luffy's fruit Gum Gum no me and it's various attacks which Luffy will develop in the future.
One day Ace abandon Luffy who gets captured in the hands of Porchemy of the Bluejam Pirates which were searching for Ace. Luffy with all his willpower refused to give out any info regarding Ace and sabo. Seeing Luffy like this and realizing the situation Ace along with sabo rush to rescue Luffy from the hands of Porchemy, Ace failing to use the element of surprise was about to be attacked when Leo appeared out of nowhere in front of him blocking all attacks on Ace and pushed back the attacker, Sabo using the momentum attack Porchemy from behind as Ace who after recovering from the shock have rescued Luffy and then using the opportunity to run away.
The trio ran away in the meantime Leo pretended to have a tough time also followed after time shortly.
Ace who was questioning Luffy suddenly felt a slap across his face and went on the ground after flying a distance, then went on to slap the other two who were watching from the sidelines with there mouth in the shape of O.
Leaving them on the ground Leo walked away.
After the incident, the trio becomes close with each other which after some time leads Sabo to move in together with Ace and Luffy.
Meanwhile, Leo started learning observation Haki which was collected from the Marines headquarters by the shadow unit which had infiltrated it earlier, Using his mind into a singular task at full capacity, Leo sat in the same place for more than 4 months watching even the tiniest details of water falling from the leaf or a caterpillar moving slowly Villagers down below the mountain doing their daily life activity. Little by little expending the range of his Observation Haki.
Arcnologia due to exemplary results were selected to be bought into Top academic class where the kids who either had High potential and are on the track of becoming become a top leader within Marines in the future or the relatives of Higher up within Marine who wanted to use nepotism to provide best for their relative and wellwishers. He was also adopted by the Vice-admiral which had earlier picked him up. With Hope in charge of everything as a Moderator, everyone did their task without requiring any assistance from Leo.
Leo after practicing observation Haki for 4 months decided to develop his sword style. Using the Arc of embodiment and observation Haki, Leo started practicing the sword artwork he was already very proficient in various kinds of Sword fighting styles due to his experience in SAO and Naruto world but he regardless decided to incorporated a new single-handed style which worked with the techniques his team has collected for him. Leo's team has already collected all the techniques whether they are of CP branch of Marine or the fighting and sword style of the likes of Shark and his crew who didn't eat a devil fruit and sole relied on various skill and fighting styles. Probes in the sky in invisible form spied on everyone stealing everything which was deemed useful.
Hope from time to time informed Leo about the trio causing troubles or fighting each other, Leo without any mercy always beaten them and when Luffy and others would complain about it he would just say this is his fist of love. Soon one day Hope informed Leo that Ace had stolen the wine from Curly Dadan. Seeing this Leo moved where Luffy and Sabo were, soon Ace arrived and was surprised to see Leo also present here, Giving a big smile Ace came forward taking out 4 small cups and purposed the cup of sake for brotherhood for life, seeing all three smiling like Idiotes Leo also giving a small smile to both Luffy and Sabo and said in a low voice: As we today take this vow, I as your big brother will always be there for you three. Hearing this the trio started laughing loudly like idiots again, feeling embarrassed Leo punched all three again and disappeared in thin air again.
With everything over Leo decided to go out. He went to Dadan family informing them he is leaving while also leaving notes for the three newly made brothers of his stating that as big brother He has to get stronger quickly to protect the three thus have decided to leave the island and go on to explore the world also stating that they too should leave when they reach the age of 17 and that he will be waiting for their name to be heard.
With the things with the trio completing, Leo moved onto one of the Helicarrier which was closest and was working on the genetic mapping of different species which morphed into a higher form of life due to exposer of heavenly energy.
Everyone within the alliance was already a war veteran was had fought at least 2 or more war during their lifetime in Naruto world and were very interested in learning Haki and such thus everyone including the people who previously chose to stay within the world seed came into being and started training on their own. Many have already claimed fruits which were found by the teams, Leo had already declared that the timeline of the original story should not be derailed thus the fruits which were shown throughout the series till the Battle of Marinefort were left untouched while rest found were either collected or were put under observation by the alliance. The battle of Marinefort was when Leo and his team which wants to take part will appear in front of the world.
With the period of 9 years remaining before anything remotely interesting happening, Leo and the rest of the 10 Helicarrier who weren't assigned any tasks moved near the bubble as near it almost all life was the extent and powerful beast could be found to train on it.
The forces selected a group of 7 islands with 1 island located in the middle. The forces took over the 7 islands whereas Leo alone ventured into the 1 island in the middle which had the most powerful beast and such out of all. Leo with his Arc of embodiment and Rinnegan didn't have anything to fear in regards to death. But he chose to just use Haki and his gunbai while fighting through the Island. Each Island was different, one was such that it was covered in the snowstorm which was falling from Sky itself. The second was covered in Black lightning which was falling unpredictably, Third was a volcano range with one or more volcano always overflowing the island, 4 was similar to the sky island everything was huge trees animals beats everything, 5 was coved in thick mist it was the home of silent Monkey evolved tribe which could kill anything which moves within the island and eat it, and 6 island of the series of the group the Island of water were the island was just a deep well with mysterious beasts inside it the beast was made infused with sea stone and other rare materials within their bodies the uppermost layer of the island seemed like a fog ground by in reality was hiding the beast underneath which can attack you from any direction in any manner. the destroyed fog would automatically return and land would turn back into the wet sand.
The middle island consisted of the beast which could be described as the top of the food chain with even the likes of 4 emperors of the new world being either weak or somewhat equal to them. Seeing this Leo and the alliance chose an island which they felt was most suitable for them and started their training. Teams were regularly changed so that even the people who were out working on the task given to them also came and practice on the islands.
8 years pass by quickly, only around 200 people weren't able to unlock of Conquer Haki, Defense perimeters where made around the 7 islands out of sea stones and such which would require a particular way for anyone to enter the middle island where Logan build a city in which each building was designed as per the needs of everyone. Leo at first assigned areas to everyone and later created Houses which they have made submitted proposal of using Arc of embodiment. In the middle was the tower of Leo, it was made out of glass-like structure through which like a two-way mirror, Leo could see everything but the outside world only saw their reflection. A training area was also designed in which various people can come together and fight each other to resolve issues and train together. An AI specifically made by Hope was designated to everyone which would rule on all the fighting and Judgements.
Shinobis had a higher concentration with a tendency to be patient and focused thus fighting among themselves was almost nil. Clan and village divisions were already washed off thus individual member's achievements and work was taken into consideration. His 7 island nation didn't lack any resource due to him having Ace of embodiment, everyone was happy and focused solely on Training.
After 8 years and the establishment of the cities, 8 out of 11 teams looking for devil fruit returned with more than 4000 fruits with them of various kinds which were not part of the cannon and were mostly lost or hidden away from the world. To make everything fair and just, and important to keep the forces motivated as some were just focusing on the research on genetics which they found fascinating Leo announced a fighting competition to be held every 5 days in which winner gets a devil fruit of their choice.
The competition leads to active participation among everyone, due everyone been grown up infighting was less than what Leo expected. Leo also announced that 2 forces will be formed in which the leader will be decided by competition which will be held in 2 years, both the finalist and the runnerup will be the vice-captain of the pirate crew which will be formed in the future.
The participation increased, Leo also fought with various people in various things, swords, gun manship, Fish-Man karate, Haki fight such as a person will wear a blindfold while other will attack using whatever they wish to use for the attack, Death was virtually impossible as Hope would always upload the conciseness of the person back into the world seed if the damage is done is more than what nanotech can heal.
In the other side world soon after Leo left, the trio made a promise to train and find Leo in the future. Soon the incident with Sabo happened to leave Ace and Luffy feeling helpless, motivating them further. 6 years went by Ace leaving Luffy behind and started his journey becoming famous quickly while being offered the position of a Shichibuka which he rejected and later went on to fight and then join whitebeard after his defeat.
Leo knowing the story declared that the forces will in 6 years one will go and finish Big mom while then second will go on to fight Kiado. Uchiha Madara of the Village Hidden in the leaf and Ranju Zabara from the warring state era Zabara clan were the two individuals who both got into the finals of the ranking tournament. With Ranju selecting Goro Goro no mi fruit which would in the future be taken from Enel when he fulfills his purpose within the arc. While Uchiha Madara wanted his Gunbai which was specially created out of sea stones, as for the fruit he didn't have any preference so Leo decided to give him a Mystic Zoan fruit which was specially created in his research the model was based on the Kiado's dragon fruit and Whitebeard first commander Marco Tori Tori no Mi, Model: Phoenix, Giving an appearance of a Kun Peng which had a mouth of a dragon and back made out of sea fish making it more adaptable to water element while having 2 wings which could collect the moisture in the atmosphere and attack as a water ball and 2 hawk-like hands. The research team has identified the way to upgrade a normal Zoan fruit as per the need, unlike the SMILE Kaido used. Research regarding other types was going on too. Many fruits were created but not consumed Leo wanted a perfect fruit with no side effects as the matter was related to a person's soul.
Leo himself didn't take any fruit but only relied upon Haki like Garp to fight. Leo in the meanwhile also started learning how to cook by watching various techniques that were collected in the huge data compilation from all around the world.
His half of the shadow team which he had sent to the moon returned about 7 years ago carrying various information regarding the technology of the world and their advancement made by the previous generations. Robot-like creatures by the name of automata were also brought back, which Leo along with other upgraded to serve as basic servents which would world from all sectors such as house cleaner to security, they had an appearance of Little dwarf humans children, which were modified as per the need of the duty assigned to them, they didn't need energy as they consumed the heavenly energy within the surrounding to work. Making Leo understand the workings of the heavenly law more clearly.
Meanwhile, the outside world, the original storyline went as usual which the slight change of Arcnologia become a direct discipline, Garp, with the request of Fleet admiral Sengoku who along regarded Arcnologia talent very much. Arcnologia under the guidance of Garp started training in the 6 Rokushiki.
Leo along with the rest of the force already has the body structure of a peak human in terms of super strength and such due to nanotech in their body which modified their body in such condition and kept them in such have already started practicing the Rokushiki and also incorporate them within their fighting style. Fruits that were seen valuable in the hands of Marine were also collected.
The second half of the shadow unit which was sent into the Marine and had spread the nanotech throughout the Marin was instructed by Leo to use any means to enter the CP units which worked for the World Government directly. Around 11 people from the Shadow unit were selected to do so information regarding the orphan children who were going to be selected was collected from the information pot which was planted on each island Leo made the identical meat suit as those children uploaded the consciousness of those 11 selected was uploaded. All 11 were placed within the selected batch of orphan which were going to go through the selection and then brainwash session of the world government before being trained to serve as an assassin for the world government.