More story more spoilers! Don't say I didn't warn you!
*** Spoiler - click to reveal ***Now I immediately began the mission Pompeius Magnus after killing The Scarab.
However I think that this mission will trigger after you have killed the first of the four new targets. Let me know in the comments if this is the case.
EDIT: I believe you now do need to kill The Scarab first. Thanks to MCutshaw0723 for the comment mentioning that he kills the Hyena first, but does not proceed straight to this mission.
This time you play as Aya, follow the mission objects through, it is completely linear. After you save Pompei's octareme a cutscene will play and then throw you back into the main game.
Your achievement should pop shortly after loading back in.
Let's keep cheevin' Together!