Shukaku: No, the New Kingdom missions are split into pathways of either "no invasions" or "lots of invasions". The choice you make in the second mission selector (Byblos or Baki) decides the end game mission you will play however.
None of the missions in the New Kingdom have any relevance to the Cleopatra expansion and don't lead to it, as those missions were designed before the Cleo expansion was considered. Therefore, completing the New Kingdom does NOT lead directly into the Cleo expansion and it must be played separately.
It's this non-linear, You say? So now that I have chosen Byblos (military-related), the third and mission of the game will be automatically military related? And if next I choose city building, the final one will be all about building a 12 000 city?
Hmmm, interesting. Well, Thanks for these information - For now I am going to finish the base.
Yeah, after 15 bloody years, I am going to finally complete Pharaoh!