Ghost Bear's Legacy takes place after the Refusal War, and is the story of a new Ghost Bear warrior living in the Inner Sphere who initially repels raids by mercenaries but is enraged when the Draconis Combine steals the genetic material of the Clan founders Hans Ole Jorgensson and Sandra Tseng. The Ghost Bears send units to track down the culprits but find the matter is more complex than they first thought. The Draconis Combine has been framed for the raids and the BattleMechs used in the raid were captured by Clan Smoke Jaguar several months before. A search through the Clans for the culprit ensues.

It is found the Smoke Jaguars lost the BattleMechs in a raid by Clan Wolf. After the Refusal War, the Wolf Clan divided into the Crusader faction under Khan Vlad Ward and the Warden faction. Sending units to investigate, it ts soon discovered the Jade wolves, two rogue Galaxy Commanders of the Crusader Clan Wolf, stole the materiel in the fake raid. The Wolves allow the units sent to investigate Clan Wolf in Exile to honorably withdraw and the stage is set for the final battle.