Clear Skies follows a trio of down-and-out misfits who've seen no end of bad luck. John Rourke is the obstinate captain of the Clear Skies, a Tempest class battleship manufactured by the downtrodden Minmatar race of New Eden. Rourke's attitude toward his hazardous chosen lifestyle is cavalier, although this does not sit well with his friends among the crew.

Trapped in the padded white room of an abandoned asylum, a helpless man awakens, only to find himself chained down to a medical chair. There, a demented surgeon and his equally deranged assistant embark on a seemingly endless series of chirurgical tortures, unlocking new levels of pain and suffering, one excruciating procedure after another. Intent on harvesting the captive's endorphin-infused blood, the maniacal doctor mutilates the feeble flesh and breaks the naked bones, until the phial is filled with the life-giving substance. However, in this hellish purgatory of anguish and torment, the man finds the strength to cling to hope, as he keeps finding hand-written notes in his grim cell. Could there be another tormented patient in this nightmarish facility? Is there an escape from the never-ending agony?