Basically this game is set around the time of 3067. The Fedcom Civil War is raging between Archon Katherine Steiner-Davion and her brother Victor Steiner-Davion.
The pro Katherine side are Steiner loyalists and their powerbase is largely in the old Lyran Commonwealth. Victor is made up of Davionists who are mostly sympathetic to the Federated Suns/Commonwealth. (I am NOT going to explain all of Battletechs rich political history)
Into this, steps you. The Commander of a newly formed Mercenary Company. First off you choose a sponsor Mercenary house. These four choices will be well known to Battletech players.
They are The Kell Hounds, the Wolf's Dragoons, the Northwind Highlanders, and the Gray Death Legion. Each side has it's own particular advantages and disadvantages. Each side also has has it's own thoughts on the Fedcom civil war.
Taking a mission and completing it will boost your reputation as a mercenary, but also taking missions from either House Davion or Steiner will boost your reputation with them to the detriment of the other.
The Clan and Inner Sphere mech packs from MW4: Vengeance are also useable here.