Under the employment of Griffin, the Commander is an associate of Doctor Persica's and has plenty of experience in electronic warfare.
In 2063, at Doctor Persica's behest, the Commander started investigating Griffin Dolls that originated in 42Lab and discovered the incident that occurred to Project Neural Cloud.
To further investigate the events, Doctor Persica digitized the Commander's consciousness and uploaded it to Magrasea. Using the "Professor's" privileges as the person-in-charge of Project Neural Cloud, the Commander embarks on a journey to search for the missing Dolls and find the real Professor's whereabouts.
Having arrived in Magrasea, the Commander assumes the Professor's identity to activate the Oasis Sector as a base and starts gathering the Exiles.