Egypt's power has crumbled and collapsed, leading to a civil war! Throwing the hat in with the legitimate heir's to the throne, your family must rebuild and defend the Inyotef's home city of Waset and provide the country with troops or succor as necessary...
Waset is probably the easier mission to choose from in the Civil War, simply due to the lack of any real threat to the city. Henen-nesw will randomly threaten your city at the beginning and send a really weak army to invade which can be dealt with by just using two or three Warship Wharves. Plus, there are many goods available in the mission which can be exported for a good amount of cash. However, you will have to import 3 required goods to evolve the housing, which are Papyrus, Beer and Linen.
The settlement should be started in the North, next to the ore bearing rock. In the southern part of this ore rock, build as many copper mines as possible and get rich selling it to Thinis for a starting export. Don't take too long to build your city, for Thinis will continually request food from you and it will start pretty quickly. Use a Ferry Landing to access the farmland on the Western bank and build loads of Grain and Fig Farms. Build a tiny settlement next to the small stream of water on the west of the map to support a Water Lift (4 single tile houses with a Firehouse and Architect's Post will be fine) and irrigate the farmland to increase crop yield. Make sure all food you produce goes into a Storage Yard to send off to Thinis. Build about 4 Fishing Wharves in the limited space in the north of the Nile (you'll have to build a tower to sterilise the crocodile spawn area).
The small island in the south of the map should be used to harbour clay, pottery and warships. Try to overproduce pottery and clay in the mission as it can be sold to nearby cities (straw from the grain farms can be used in conjunction with clay to produce bricks and be sold to Men-nefer for an additional boost to the treasury).
Don't neglect your military! It won't be long before Thinis will start demanding troops from you. I recommend two infantry and archer forts, all 4 being academy trained. That alone will be enough to deal with the threat to Thinis (the second troop request gives you 2 years to deal with it). A few warships will be enough to deal with the threat from Henen-nesw when they attempt to attack you by water.
Eventually, you'll want to build the pyramid and Sun Temple. The Pyramid is probably the easiest to build as the materials to build it can be quarried in Waset. You'll have to import Wood from either Dunqul or Dakhla Oasis though. Since Dunqul has the more trading options available (Dunqul sells you Wood, Gems and Sandstone and they purchase Clay and Pottery but Dakhla just sells Wood and buys Luxury Goods), it is highly recommended to not bother opening up the Dakhla Oasis trade route and go with the cheaper Dunqul Oasis route. It's also a good idea to open up this trade route early so you can import wood to build your warships.
The Sun Temple should be built last as it requires a lot of imported Sandstone from Dunqul Oasis. It might be best to build this on the western bank as most of the eastern bank will consist of the bulk of your city. Once the Sun Temple is built, you should be closing in on the mission requirements and be completing the mission!
This part shows the build up of the city, defending the city from Henen-nesw, as well as sending troops to defend Thinis. We also get the exports started, while having a tough time with a lack of workers, due to all the required buildings being built too early, along with starting on the pyramid and manor area. Next part will cover the completion of the pyramid and the Sun Temple.