I have to admit, I shouldn’t take credit for this theory, as a former Nerds4Life writer and friend of mine, was the one who first introduced me to this possibility, Furthermore, the more that we see Boruto and Momoshiki’s control over him, the more this theory is a serious possibility.
When Boruto first began, we watched as two teenage ninja’s engaged in a fight over the ruins of Konoha, both wielding powers that we knew nothing about. In this brief glimpse into the future, we watched as the son of the Seventh Hokage attacked an unknown boy named Kawaki, who clearly was his former friend. However, we have learned more about these characters since that point and that’s why I no longer feel that Kawaki is the villain in this scene.
It’s actually more of a possibility that Boruto Uzumaki is the one who has attacked Konoha. We have already seen that when Momoshiki releases himself from within Boruto, the young ninja loses all control and in the last chapter, even stabs Sasuke. In addition, unlike the demon within Naruto, there is no way that Momoshiki will allow himself to be be-friended like Kurama.
Therefore, Momoshiki will slowly continue to take over Boruto’s body using the Karma mark and that means that Boruto might increasingly lose control. it’s possible that Boruto is the one who has lost control in Konoha and therefore, was the one who brought it to its destruction. This means that Kawaki will continue to be Naruto’s student and is the one trying to stop Boruto from harming Konoha’s citizens more.
However, there are two flaws to this theory. Where did Kawaki get another Karma mark from and what did he mean when he told Boruto that he will do to Boruto what he has done to Naruto? Well, the first one could be that Naruto isn’t in control of himself and is also being used as a weapon. We already know that Baryon Mode had stripped him of many years of his life. If Naruto dies prior to this and is then reanimated, it’s possible that he could be used as a weapon against Konoha and Kawaki simply sealed him away.
If Boruto is out of control, Kawaki might be trying to seal him away too while he is in Momoshiki’s possession. This is what he might mean by doing the same to Boruto as what he did to Kawaki. Then, there’s the issue of how Kawaki was able to get another Karma mark. It’s doubtful that it’s through Isshiki, as it appears as if he has been defeated without transferring another mark. So, he must get it from somewhere else that we just don’t know of yet. Maybe it’s from Toneri who we know is an ally to Konoha now, as seen in the anime when he was sealed. If Toneri was able to escape this fate, it’s possible that he might lend his powers to Kawaki in order to help Boruto.