WARNING: The following contains spoilers for Chapter #51, “Sacrifice,” of Boruto: Naruto Next Generations by Masashi Kishimoto, Mikio Ikemoto, Ukyo Kocachi, Mari Morimoto and Snir Aharon, now available from Viz Media.
The latest chapter of Boruto has given some much-needed insight into the Ōtsutsuki civil war we didn't know occurred during the Naruto series. It turns out that Kaguya betrayed Isshiki because she didn't want to be the sacrifice fed to the God Tree, just so it could bear chakra fruit for Isshiki to eat. She instead chose to kill him so she could have the fruit to herself, however, given the rules of the alien clan, her sinister plan was way too complicated and, ultimately, doesn't make much sense at all.
If Isshiki could've used his Karma mark to be reborn into Jigen and Kawaki, then Kaguya simply could have used a vessel to do the same. Isshiki's current plan is for Jigen's body -- with him inside -- to be devoured, thus allowing the God Tree to bear fruit, with his rebirth into Kawaki's body then allowing him to eat the fruit. Basically, he's feeding himself to the tree and using his Karma Mark to come back to life.
Thus, if Kaguya was sacrificed, she could simply have been reborn into someone else's body, similar to Isshiki's own plan. Once she was eaten, she could have used her rebirth to then kill Isshiki and get the fruit all to herself. This fruit would have been much stronger as she'd have fed the tree her fully-powered self as well. All she had to do was play the long con and use Isshiki, duping him into thinking she was falling in line.
This also proves her ultimate rebirth in Naruto far more complex than it needed to be. She left her will behind in the form of Black Zetsu, enacting a long-winded scheme that involved manipulating Madara and Obito Uchiha, the Akatsuki and many shinobi nations. There was so much room for error -- as seen when Kabuto and Orochimaru inadvertently nearly botched her resurrection with their own experiments. But because of plot convenience, the right dominoes were knocked over, allowing the Rabbit Princess to return to life. Still, Sasuke, Sakura and Naruto fought and sealed her away, leaving her with no more contingency plans.
This could have been avoided if she perfected the Karma Mark initially and passed it down to a cult or a proper vessel so that when her own sons, Hagoromo and Hamura (Naruto and Sasuke's ancestors), sealed her away, Kaguya could be reborn.
Seriously, this Karma Mark is a "get out of jail free" card and all she needed was some patience. It'd have been much easier than orchestrating a centuries-long conspiracy. Even if she didn't know how to create the mark, Isshiki could have taught her. This way she could be reborn over and over, becoming immortal by feeding chakra-infused humans to the God Tree to bear fruit. But rather than implanting Karma, she lacked foresight and acted more on emotion than logic, as seen when she blindsided Isshiki and ultimately, doomed herself.
