When Naruto arrived at the Feudal Era, he had enlisted the aid of the undead priestess Kikyo at his side. They both traveled around the world, aiding people along the way on every village they traveled. As such, they have both been praised by the lords and the common folk alike.
Naruto has proposed that they'd find a Basculus which is the only one of its kind since no such objects exist in this era. They found an ancient temple guarded by Naraku and used necromancy to create an undead golem to distract the security. Once inside, they have discovered that Naraku had slew a number of Naruto's fellow gods during his visit there. It is Kikyo's duty to track them down and bring them peace. They have found the souls of Kiba, Shino, Neji, Tenten, Ino, Shikamaru and Chouji where Kikyo used her words of purification to bring them peace back to heavens.
They have found what they have been looking for when they entered one final chamber. The last two surviving gods, Sasuke and Sakura explained that Naraku had tainted the Basculus but Sakura cured it while Sasuke barely drive Naraku away with his powers, leaving them both drained.
Naruto decided to shown kindness to them by telling Kikyo to heal their wounds. When Sakura asked, Naruto answered that they owe him now and he would ask them for aid in the future. With that finished, Naruto took the Basculus and left with Kikyo.
On their way to a village, Naruto and Kikyo encountered Inuyasha and his friends. They both sense tension of the group aimed at Inuyasha but decided to ignore it as it is not their concern.
It proved to be a mistake.
In one night, during his walks and fondling his Basculus, Naruto had overheard Kagome angrily guilt tripping Inuyasha and tearfully telling him that she doesn't want to see him again. It turns out from what Kikyo told him that Inuyasha had been going with Sango and establishing a relationship with her and accidentally cheating on Kagome. It got worse as Sango told Miroku and Shippo about Kagome's departure and needless to say that they didn't take it well and left Sango and Inuyasha to their fate.
With this small but significant wrongdoing, Inuyasha's group is split and broken. And what's worse is that Naraku didn't need to do a thing. Inuyasha and Sango destroyed the friendship and trust of their loved ones on their own.
Naruto and Kikyo continued their travels and fought Naraku. Thankfully Sasuke and Sakura repaid the favor they owed Naruto by aiding him against Naraku. Realizing that he was outmatched, Naraku was forced to retreat.
Sakura told Naruto that she had freed Kohaku from Naraku's clutches while Sasuke told him that he had engaged Naraku's servants -Kagura and Kanna- and destroyed them with great effort, Naruto expressed his thanks and told them that he owed them now.
Sasuke, Sakura and Naruto parted ways again and decided in their own way to do what they can stave Naraku's influence throughout this era. Despite their best efforts, Naruto and Kikyo's actions can only take so far and the villagers suddenly turned on their feudal lords for some reason. Naruto and Kikyo barely kept the chaos from going out of control as the people in every village turned on each other like wild animals.
What's worse is that Inuyasha was killed through crucifixion and while Sakura delivered Kohaku to his sister, the reunion was short lived as the villagers believed that Sango is also a demon despite her profession and her brother is also guilty by association. Naruto and Kikyo got to them in time before the villagers could and secretly escorted them away from the village they are staying in.
With Sango's credibility as a demon slayer stained because of her relationship with Inuyasha, she had no choice but to stay with Naruto and Kikyo. Same applies with Kohaku.
Miroku and Shippo continued traveling together until they settled down in a village where they've both been told that Inuyasha died via crucifixion and they have driven Sango 'the demon whore' away. They just nodded along as they didn't want to get on the villager's bad side.
Kagome stayed at the modern era, watching the news as it says that the climate is changing for the worse, all types of natural calamities are preparing to be unleashed on earth though thankfully they hadn't hit any major city yet. She mentally berated herself for not being strong enough for Inuyasha and planned to return to the feudal era.
In the meantime, a fanatic sect of monks began a worldwide purge of demons. It served its purpose for a time then infighting spilled over the group as there are a good number of monks who are sympathetic to the more helpful type of demons. Naraku -in disguise- used this opportunity to widen the cracks of distrust amongst the monks and it ultimately destroyed them. This sect disappeared and is never heard of again.
Naraku gathered a massive amount of demons and invaded the villages. Ill-prepared and leaderless, the villages easily succumbed to the invasion and any defense they tried to amount was quickly flattened.
Kaede managed to recruit both Shippo and Miroku and told them to warn the other villages of Naraku's threat. They did so but the feudal lords merely scoffed at it. It work take a few days before they realized their mistake.
In desperation, Kaede asked the two to contact Naruto which they did and he accepted. The reunion with Sango and Miroku and Shippo went coldly but they had to set aside their differences in order to stand a chance against Naraku.
Two years later, Naraku was eventually defeated thanks to Sasuke and Sakura's efforts but his death triggered a madness that driven the demons to attack the villages in a frenzy. The three gods as well as Kikyo, Sango, Miroku and Shippo tried their best to defend against them but they were too many, so many that it looked like the sand of a desert.
In the back of his mind, Naruto wondered where Kagome was and where the hell did she not go this era yet?! He had to put off that question as he saw his fellow goddess Sakura pushing herself harder and harder to protect the retreating villagers from the demons only to be overwhelmed. Both Sasuke and Naruto saved her but the damage they had done to her was terrible. Sakura urged them both to leave her behind and protect the last village -Kaede's village- and fortify it with themselves. She would hold the line and buy them enough time to mount a last stand against the demons so that humanity may have a chance.
They reluctantly agreed and Sakura impressively killed 9,999 demons before finally being overwhelmed. Her bravery allowed Kaede's village to be fortified and ready for a prolonged assault.
The final battle began five days after Sakura's death and Kagome finally arrived on the next day in order help. Needless to say, Sasuke wasn't pleased that she was late and even went as far as to say that Sakura -a goddess- would have been alive had she arrived sooner. He even called her a coward and a procrastinator and would have attacked her had Naruto reasonably told his angry colleague of a god that they need all the help they can get.
The battle raged for days and the human's numbers began dwindling by the minutes and the demons slowly overwhelming the humans. Kaede was saved by Kikyo who took a sharp talon to the chest meant for her. Kagome protected Shippo but was too late to assist Kikyo who was dying and cared for her in the undead priestess' final moments.
Seeing his loyal servant and soon to be lover dying, Naruto went into a rage, killing thousands of demons with forests and tornadoes. Through his rage alone, Naruto saved the world and Sasuke wiped out the rest with his meteors.
Naruto tended to Kikyo and revealed all his feelings to her, telling her that he loved her and he couldn't bear to see her die. He gave her one deep, final kiss before she passed away. In his grief, Naruto angrily blamed both Kagome and Kaede and declared that while he will let them have their spiritual powers, he would NOT see them again and even went as far as to say that the next time they call him, they should expect to be impaled by a wood branch. He and Sasuke left as they both came to an understanding that they have both been united in their shared but highly illogical hate against Kagome.
The remaining humans were relieved that this armageddon is over but realized that it had cost them all but their lives. Still their resiliency and passion urged them to start rebuilding villages and their homes and paid off now that demons are officially extinct.
For Kaede, she redeemed herself by curing a boy off a demon that was infecting him at the cost of her own life.
Kagome was hurt by the fact that she made a mistake leaving Inuyasha that have cost him his life. And with Sasuke leaving for parts unknown and Naruto refusing further contact with her, she set out to mend burnt bridges with Sango who accepted and even made Shippo and Miroku bury the hatchet with her as they discovered that Kohaku had been crippled and could never be a demon slayer again.
Both gods -Naruto and Sasuke- went their separate ways but both promised to come to the aid of another when they need it.
Inuyasha was buried by Kikyo and Naruto before the invasion but a red lightning spark suddenly hit his grave...
Inuyasha rose from his grave and has returned...
Notes
This is not written as a regular story but a synopsis rewrite of the same title. This is basically a summary of that rewrite and there will not be a sequel.