Once you click Begin Mission on the main menu, you will be displayed a world map. This map shows which regions are controlled by a given syndicate. If you control a given country, you can set it's tax rate, either to get additional funds, or to prevent a rebellion within that region.
At the start of the game, the only region you can act upon is Western Europe, which is selected by default. As you conquer territories, you will be able to enter additional regions.
If you overtax a given region, the people within that region will become unhappy, and eventually rebel. The result is that you need to redo the mission in that area.
The briefing for a given region is shown as soon as you click Brief. You are shown the mission objectives on the left, and may either accept the mission or return to the map to select a different area. You can also review the map, and scroll around it to see how to plan your assault.
If desired, you can purchase additional information, which adds a tactical analysis and hints to the briefing. You can also purchase a scanner enhancement, allowing you to view more of the map at once.
In the equipment screen, you can select upto four agents for your mission. You can purchase or sell any items (including the free pistols), and head to the mods screen in order to apply cybernetic enhancements to your agents.
Research is accessed from the equipment screen. From here, you can assign your scientists to investigate both items and improved cybernetic modules.
After selecting a category on the left, you are presented with the minimum and maximum research cost for a given item. When approved for research, minimal funding will be automatically assigned, allowing research to be completed in 10 days. Additional funds may be allocated to increase the rate of research; in most cases, you only need to set research for 5 days or possible one level faster on the easy missions, which should allow it to be completed after you return from a mission.
New items that are collected during the mission will be assigned to the research department. This will complete about 30% of the research required for the item.