It all started when Shadow Spider spoke to you about a theft which occurred at a high-profile Arachnos base. Judging by the way the Arachnos guard were taken care of, Shadow Spider suspected the Knives of Artemis. Since Malta works closely with the Knives, Shadow Spider sent you to find more information by invading a local Malta base. You discovered a Knives of Artemis sisterhood led by Aurelia Nine had taken the contract against Arachnos with an unnamed private party from St. Martial, and learned the location of Aurelia Nine's temporary base.
Traveling to St. Martial, you hit the warehouse and tracked down Aurelia Nine. She related how she did further digging into the private party she took the contract with and discovered he was actually a deep-cover Longbow agent code-named 'Crimson'. Shadow Spider heard of him, and realized it wasn't going to be easy taking him down.
Traveling to Agent Crimson's secret hideout in St. Martial, you tracked him to the sewers underneath an office building there for a final showdown.