Boruto: Two Blue Vortex has been grappling with the power dynamic between Kawaki and the main protagonist ever since the first chapter. Eida's Omnipotence managed to turn almost the entirety of Hidden Leaf into Kawaki's allies, while the main protagonist became a fugitive. However, the actual long-term effects and the resistance shown by a few characters have become the focus of the story.
Characters like Himawari, Sarada, and Shikamaru have already shown some form of resistance to the effects of Omnipotence, further foreshadowing a divide within the management of Hidden Leaf regarding their stance on Naruto's actual son.
While nothing has been confirmed yet, chapter 14's sneak peek revealed that Sakura will be returning to the story to heal Ino's son. It is possible that both of them may end up supporting the protagonist, while taking a stance against the rest of Hidden Leaf.
Disclaimer: This article contains spoilers for the Boruto Two Blue Vortex series.
Boruto: Two Blue Vortex: Inojin will be the key to undoing Omnipotence
Eida's Omnipotence and the memory alteration of everyone except the protagonist and Kawaki, were the main events that led to the storyline of Blue Vortex.
While the actual nature and process behind Eida's Omnipotence have not been revealed, given its status as a near-divine technique, it is possible that the technique manipulates the chakra inside people's bodies and essentially acts as a lifelong genjutsu, constantly manipulating memories.
Genjutsu works on a similar principle, relying on the manipulation and disruption of its target's chakra to influence the five senses, eventually leading to typical illusions. In essence, Omnipotence might just be a technique similar to genjutsu, which becomes fully automatic once activated.
Similar to every other jutsu, Omnipotence would also need a source of chakra, which might be the natural energy that forms the basis of Sage techniques, given that Omnipotence possibly runs indefinitely throughout the world.
Inojin almost died at the hands of Jura, and his status was confirmed in chapter 14 sneak peeks with Sakura healing him. It is possible that Inojin became disconnected from the natural chakra around him, and thus, he might wake up with the correct memories of Boruto being Naruto's actual son.
Sakura, being his healer, might dismiss Inojin's claims as him having a hazy mind after nearly dying. However, Sakura's close association with the now-missing Sasuke and the "dead" Naruto might lead her to investigate Inojin's claims further, eventually noticing the chakra disturbance that tries to suppress doubts and inconsistencies regarding altered memories.
Given Sakura's status as one of the three shinobi who were directly responsible for Kaguya's defeat, it is possible she will become Boruto's ally, and convince other doubtful Hidden Leaf members to aid the protagonist instead of Kawaki..
Final Thoughts
The actual direction of the conflict has not been solidified as of Boruto: Two Blue Vortex chapter 13, but the protagonist's status as the sole resistance against the Shinju, as well as his overwhelming knowledge of the current events, necessitates his survival.
It is possible that many of his supporters will aid him in escaping, which might eventually result in Kawaki forcibly taking over the entire village and paving the way for the "War arc" that is anticipated by many fans.
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