I think Scar became Charon the monolith commander found in Pripyat in SoC because:
1. Most obvious reason, his loadout is the exact same as Scar potrayed in wallpapers and promotions.
2. Scar along with Strelok we're affected by the emission at the end of Clear Sky, Strelok miraculously escapes but I think Scar was affected and turned into a monolith soldier.
3. Why would Scar become the new commander? Because his fighting and tactics got him all the way through the zone by himself.
4. How come Strelok esacped the final emmision, my theory is because Strelok had a reason to be himself in the zone. The C-Con let him go because they knew there was a reason for him to be himself in his own ways. Scar on the other hand was just a hired fighter taking orders.
What do you think?