For a more detailed walkthrough, see New Walkthrough by themousemaster1.
Before we begin, we might want to brush up on some basic strategies first.
Campaign 1 - Alpha
Your team is assigned to the Western Sector to locate and retrieve Pre-Collapse technology. Your main goal is to find the Synaptic Link Technology. The Western Sector is a barren wasteland with dry ground and little vegetation, broken up by ridges and plateaus. Because you're a new commander, you're assigned the easiest of the three sectors.
As a part of this campaign, first build a base, then explore the surrounding area for new technologies. You'll run into Scavengers and other enemies, so be careful. Some missions require you to take an away team to a distant area of the sector by transport. Even though you're away from your base, you can still give manufacturing orders and research new technologies.
Campaign 2 - Beta
Beta Team has established a base in the sector, but has done very little expansion. The Collective has declared war on the project and is determined to drive your forces from the sector. Your objective is to defend the base and then begin to eliminate this new enemy. You also must search for the VTOL (Vertical Take Off and Landing) Technology.
Campaign 3 - Gamma
Nexus has fired nuclear missiles at and destroyed Beta Base. Therefore, you must transfer your command to the Gamma Sector, in the cold, snow-covered Rocky Mountains. The key is to use the terrain to hide your units from the enemy while not getting ambushed in the process.
Nexus has all the latest and most powerful technology. Until you can capture and research some of it, your units will be at a disadvantage. The Project is depending on you, however. Your failure means the end for it.