The Puppet Masters of Boruto
Who is pulling the strings?

Longtime Naruto fans are no strangers to antagonists orchestrating events from behind the scenes. Whether it's Pain, Obito, Madara, or Black Zetsu, momentum in the plot is often set into motion though the actions and motivations of shady figures.
While Momoshiki played a strong part in manipulating Boruto's fate to favor his desired ends from inside our main character's head, the true mastermind of Boruto: Naruto Next Generations (NNG) appears to be Amado, the genius scientist leading innovation for the secretive organization, Kara.
Early in the plot, Amado can be read as deferential to Kara's leader, Jigen, though it's clear the human vessel controlled by Isshiki Otsutsuki did give Amado a longer lead than other members of his organization... Or, maybe not. Jigen allowed both Amado and Koji Kashin enough rope to prove they were unloyal, the Kara inners involved in a game of palace intrigue between the three while Delta smashed tables, Boro ran his cult, and Code kissed up to his Otsutsuki God.
Despite the fact that Jigen was testing both Amado and Koji, it's clear that many plot events in Boruto: NNG were engineered by Amado to favor his desired outcome: the crashed airship that allowed Kawaki to escape, Jigen's death, Isshiki's death, Kawaki embracing his karma once more to protect Naruto. Amado consistently played the odds to favor his desired outcome and achieve his ultimate end goal, the revival of his daughter Akebi.
Amado became our explainer-in-chief throughout the second half of Boruto: NNG, dropping Otsutsuki lore, their weaknesses, and the reveal of his own biotech enhancements with the DNA of the ascended Shibai Otsutsuki. And there are still open questions about the full extent of Amado's influence during the plot events in Boruto: NNG, (for example, who and what exactly was he influencing by mumbling to himself all the time).
In the beginning of Boruto: Two Blue Vortex (TBV), it feels as though Amado is positioned to play a similar role. He purposefully expresses doubts about the truth of reality while Shikamaru is listening, leading to the interim Hokage's revelations about Omnipotence. He's monitoring the world through the eyes of two of his creations, Delta and Kawaki. Even though he knows the truth of Boruto and Kawaki's reversed roles, he's still going to do everything in his power to support Kawaki, who contains the Karma for Akebi and his only hope for reviving his daughter.
But as the plot progresses and the Shinju are created, we see the baton of puppet master stealthily passed to Koji Kashin, the partner that Amado sacrificed to destroy Jigen without telling him that killing an Otsutsuki would also cost him his life. Starting with the flashback in chapter 13, Prescience, we discover Koji's god-like shinjutsu ability to see many possible, branching futures, his own variant of Eida's Seringan, Daemon's reflective abilities, and Code's transporting claw marks.
The revelation of Koji's ability pulls back the curtain on Boruto's advancement and actions through the first dozen chapters of Boruto: TBV. Boruto's abilities, knowledge, and perfect timing have all been engineered through Koji's vision of possible futures. While Boruto is a phenomenal shinobi, it's reasonable to begin to wonder if Koji is aiding Boruto or if Boruto, like so many shinobi before him, is also a tool for Koji to achieve his ends.
Koji's manipulation does not end with Boruto, however. Through Boruto, we see him influencing Kawaki to confront Amado to gain more power. Similarly, he uses a scientific ninja toad to communicate with Shikamaru and another, with Eida, to combine their shinjutsu, seeing 19 years of the past, everything happening in the present, as well as Koji's knowledge of the futures.
Koji even seems to be stepping into Amado's shoes as the main explainer of plot events, sharing just enough information with Boruto and Shikamaru about the Shinju to encourageethem follow his desired game plan while seemingly also withholding other details. This is the same pattern of behavior exhibited by Amado during the Kawaki arc before he returns in the Omnipotence arc to explain his true motives.
After chapter 19 of Boruto was released, we have to wonder how deep Koji's planning will go; he purposefully sent Sarada, Mitsuki and Konohamaru to the sand, knowing the danger he was putting them all, Konohamaru in particular into. Yet, when Boruto seems ready to jump into the fight and help them, Koji tells him, "Now is not the time," through which we can infer the possibility that Koji is trying to trigger a specific event before Boruto disrupts the fight, perhaps the death of Konohamaru, leading Sarada to master her Mangekyo Sharingan.
While Koji ascends, we see Amado slipping into chaos as the plot swings away from his area of expertise, the Otsutsuki, and into the realm of the Shinju. We see him stunned by the appearance of Jura in Konoha and admitting to Kawaki that he didn't expect them to be created. As the threats to the world (Shinju, Code, and Boruto) spurn Kawaki into action, demanding the power that Amado has been withholding from him, Amado becomes desperate to see the fruition of his plans to revive Akebi, practically begging Kawaki to revive her. Instead, Kawaki turns the tables on the man who modified him, forcing Amado to be his key to gain power because he's willing to be the door that opens and brings Amado's daughter back to the realm of the living.
Where is all this leading?
When Amado initially defected to Konoha, he framed the decision to do so as his desire to defeat Isshiki and save the world from destruction. It's not until much later that we find out his decision to do so centered around his love for his daughter rather than a selfless act.
Similarly, Koji is playing the part of a shinobi on a mission. His initial plan was to kill the Otsutsuki and save the planet from the ravages of the God Tree. He claims to be on a similar path as well now, targeting the humanoid embodiment of that same tree, the Shinju. But, in Boruto, all human motivations seem pulled toward the theme of love, and I wouldn't be surprised if the plot takes a similar turn with Koji as well. Perhaps in all those futures he saw predicting the end of the world, one of them ignited a desire in him to live and love as a human rather than a shinobi tool.
(Yes, I'm still on the DeltaKoji agenda, and I'm not getting off of it.)
There is also the possibility that Koji's motivations are more sinister, setting our two puppet masters on a collision course: Amado betrayed Koji, telling him he could kill an Otsutsuki without telling him that it would cost him his life. He created him for this purpose, gave him life for this purpose, groomed him for this purpose, treated him as an ally, and, ultimately, was disposable. Though Koji says that he was content to die until he saw visions of the future, he might be on a path of revenge against Amado... Or maybe Prescience revealed something else, and Amado, too, must be stopped.
Before wrapping up the subject of ultimate villains and the selective information they share, I'd be remiss if I didn't bring Eida into the conversation. While she hasn't been explicitly manipulating the plot (that we know of) yet, she's also another character who has a power that allows her specific knowledge of the world, and she can share intel that benefits her end goals while withholding information that contradicts them. Both Daemon's statement about Code being her "new" man and the still missing piece of the Omnipotence puzzle that will explain how her Charm ability came about from a wish in her past hint that there's a lot more to Eida's backstory that we've yet to explore. If Amado and Koji become foils for one another, she's the other character (besides, perhaps, Shibai) that has a wealth of unexplored knowledge and motivations.
I don't expect the current power imbalance in the plot to last forever. As Koji speculated, Amado probably has a shutdown code for him in addition to Kawaki and Delta. And we've already seen Amado considering the possibility that Koji is still alive and trying to deduce what he wants. But with Koji's Prescience, we should also expect that he knows what moves Amado might be devising against him and have a plan to counter them.
Wherever the plot is headed, I expect a future conflict to feature Koji and Amado, bringing together the Chekov's Gun comment in which Isshiki told Koji, "...you didn't want to acknowledge Amado's betrayal." (Chapter 48, if you want to read the exchange in full).