All these missions were played in the order that is shown below. When you have the option to chose one out of two missions, I picked the one that is shown below, the other missions are also discribed further below.

Mission number	Mission name	Mission Walkthroughs
Mission 1	The Messiah Returns	---
Mission 2	Retaliation	Click here for a detailed mission walkthrough.
Mission 3	Free Rebel Commander	Click here for a detailed mission walkthrough.
Mission 4	Destroy Hassan's Temple	Click here for a detailed mission walkthrough.
Mission 5	Eviction Notice	Click here for a detailed mission walkthrough.
Mission 6	Salvage Operation	Click here for a detailed mission walkthrough.
Mission 7	Capture Umagon	Click here for a detailed mission walkthrough.
Mission 8	Sheep's Clothing	Click here for a detailed mission walkthrough.
Mission 9	Escort Bio Trucks	Click here for a detailed mission walkthrough.
Mission 10	Destroy GDI Research Facility	Click here for a detailed mission walkthrough.
Mission 11	Villainess in Distress	Click here for a detailed mission walkthrough.
Mission 12	Establesh NOD Presence	Click here for a detailed mission walkthrough.
Mission 13	Destroy Mammoth Mk.II Prototype	Click here for a detailed mission walkthrough.
Mission 14	Capture Jake Mc. Neill	Click here for a detailed mission walkthrough.
Mission 15	Illigal Data Transfer	Click here for a detailed mission walkthrough.
Mission 16	A New Beginning	Click here for a detailed mission walkthrough.