WARNING: The following contains major spoilers for Boruto: Naruto Next Generations Chapter #51, by Masashi Kishimoto, Mikio Ikemoto and Ukyo Kodachi, available now in English from Viz Media.
The Boruto manga continues to place its titular hero in dire straits as he attempts to evade Isshiki. However, Boruto is running out of ideas as Naruto and Sasuke are struggling against the villain as well in a secret dimension Sasuke transported them to.
But as this explosive battle occurs in Chapter #51, Boruto begins to figure out why Isshiki can't murder him. Coincidentally, it ties into intel the Kara traitor, Amado, is revealing to Shikamaru, Kawaki and Naruto's science council in Konoha. And in the process, we discover the truth behind the Ōtsutsuki civil war that happened on Earth centuries ago.
In the series, we learned that Kaguya didn't come to Earth alone as the Naruto franchise suggested. Rather, Sasuke found out these aliens came in pairs but there was some mysterious reason as to why she betrayed her partner, Isshiki. He'd eventually retreat, embedding himself in a monk named Jigen, biding his time before he could strike again. His aim now is to use the Ten-Tails he's hiding and to create a God Tree just like Kaguya did, which would suck up all of Earth's energy (including its people) to create chakra fruit that these clan members can feed on; powering up, evolving and becoming immortal. That's why they go across the galaxy and drain planets, as we saw with Momoshiki and Kinshiki.
But the truth about Kaguya's dispute now emerges as Amado confirms one of the two Ōtsutsuki members arrive as a sacrifice. The junior one, in this case, (Kaguya) must be fed to the Ten-Tails, which acts as a seedling. Once it absorbs the Ōtsutsuki's energy, it then blossoms into the God Tree with chakra fruit for the other member to feed on. Apparently, Kaguya didn't want to be this sacrifice so she ambushed Isshiki, consumed the chakra fruit from a God Tree that fell to Earth, and started seeding out chakra -- which is the story of how her son, the Sage of the Six Paths, as well as Naruto and Sasuke's shinobi ancestors, came about.
Ishhiki's plan then switched up following her death, with him implanting the Karma mark in Kawaki so that once he offered himself up as Jigen, he could be eaten and reborn in Kawaki's frame. Seeing as Boruto has his own Karma mark and is transforming into Momoshiki, Isshiki wants to use him as the meal, which would leave Isshiki free to eat the chakra fruit. It's why Isshiki can't kill Boruto, because as Momoshiki, he'd be a more powerful food source than say, a diluted Jigen. This would make the fruit purer and stronger for Isshiki to level up with.
This does raise questions, though. Where did this initial God Tree seedling fell from, for instance? If it grew into a tree without a sacrifice on Earth, that means a Ten-Tails must have devoured another Ōtsutsuki somewhere to enable this to happen. Also, neither Obito nor Madara fed the Ten-Tails an Ōtsutsuki in the Naruto series for the God Tree to form. In fact, Kaguya would emerge from the Zetsu attached to Madara and then combine with the husk of the God Tree to become the Ten-Tails.
It's a bit vague how this process works. It seems the Tree can switch back and forth into the Ten-Tails, but again, Kaguya should have been killed when she merged as she needed to die to be a power source. The next chapter should explain more but at least we now know why Kaguya wanted Isshiki dead: it was all in the interest of self-preservation.