User blog comment:Master Sima Yi/Assassinews 05-08-'14 – Assassin's Creed: Rogue announced/@comment-25186657-20141201230343/@comment-13471981-20141202052849

Shay thought Achilles intended for the city to be destroyed, and Achilles doesn't really do a good job of defending himself. Even if Shay is wrong on that account, he is not wrong about the fact that the Assassins will continue pursuing these First Civilization sites, potentially putting millions of other civilians in danger, which is why he tries to steal the manuscript.

Btw, Spidermatty, if you oversimplify a storyline like that, any storyline will sound bad. It's like reducing AC3's storyline to "Where is Charles Lee?".