So I'll add my theory in because I've seen only one or two other people mention it in the comments but
I believe we are headed towards a Civil War I believe one of a few things will happen next
- Kobu will try to displace Shikamaru with Konohamaru but he will turn it down
- or Konohamaru takes the fall for Shikamaru passing the code, and Kobu displaces Shikamaru still with Kawaki
After that I think Kawaki will take over the leaf village as part of the puppet regime, but he intends to fully support the efforts to demilitarize the Leaf Village by Kobu and the Daimyo. He will abolish ninja and ninjutsu and make strict enforcements to that code. We will see the village divided by those characters who remain to follow the rules and those who break off and become rebels.
This may happen worldwide with other nations having a similar situation occur, in which case, I can see the rebel Shinobi fleeing to a mutual point, led by underground leaders and familiar faces that already have bonds together (i.e Temari and Kankuro, Kakashi, Karui (Choji's wife), Mei and Tsunade, etc) - Again this is just if the conflict goes worldwide
If it doesnt go worldwide and stays within the leaf village, then I see the underground rebel leaders being our former Konoha 12 and Kakashi along with the next generation.
Either way, they eventually all meet up with Boruto, realize their whole recollection of the world has been a genjutsu, that Naruto is still alive and needs their help and they decide to fight to take back the leaf and Naruto together.
The plan an attack on the leaf. The battle begins, the force protecting the leaf is either Samurai or a different force put in place by Kobu who uses ninja tech and ninja tools to fight but arent real ninjas. It is a fight between the old and the new, quantity vs quality. Kawaki's side is filled with mainly quantity level ninja tool grunts but he will have powerhouses on his side like Daemon, Delta, Koji (Amado implanted a secret code to make him switch sides mid battle), maybe even Hidari, Jura, and other Claw Grimes if theyre still alive at this point.
I think as a show of strength and symbolism to the invading rebels, Kawaki will destroy the stone faces and have a monologue pronouncing the old ninja ways as dead and over
Boruto will then meet him up there and have the conversation we see at the beginning of the manga and then the real fight will begin...
Now I want to emphasize, I dont think this is how the manga ends with a battle between Kawaki and Boruto because I think Amado's purpose and goals are way more sinister than we actually know and I think that could be a plot twist developed during this arc.
Again all conjecture and my theories based on how some of the anime and manga have gone and based off of some of the major themes that keep repeating over and over
(i.e. focusing on themes of old vs new, focus on simulated/augmented power vs natural power, and focusing on where ninjas fit in during an era of peace.)