Malachi Zee was born in the early 1880’s, though most details of his early life, including his nation of birth or circumstances of education and training, are unknown.   The first records of his activities are a member of the Time Trust, a collection of government scientists committing to the ending the war through fishing technology from the future.  In 1941, the Trust sought top create a bomb shield that would protect Allied powers from Germany’s increasing superiority in rocket technology.  One the members, Dr. Damon Everson, hit on the idea that the technology of the future would be vastly superior to that of the modern day and when visited by the JSA after the Trust is targeted by Axis agents, decided to send the members into the future to collect elements of the needed technology.  When the JSA had completed its efforts, the Trust was able to construct a working prototype of a “bomb shield”, a force field the repelled concussive force (All-Star Comics #10).  The others members of the Trust were not revealed until after the War and Malachi Zee is listed among them.  When the trust conducted a second test of the bomb shield, it failed (secretly sabotaged by Per Degaton) and Zee left the trust for to set up a hidden lab in the suburbs of Washington DC (revealed in America vs. the Justice Society LS).

The activities of Zee for the next several years is unknown.   In 1947, it became known that he had perfected his own version of a time travel machine, a large one able to carry humans to any time past or present.  Per Degaton remained in his employ, believing Zee had the best shot at an actual time machine.  When it was completed, Zee was ultimately doomed but in an ironic turn, his death became a temporal touch point launching the maniacal criminal career of his assistant, Degaton.   The timeline fractured when Degaton shot Zee and took control of the time Machine himself. 

At three branch points have been recorded to date.  In the first, Degaton used it to travel to the distant past, interfering with Alexander the Great at the Battle of Arbela.  The downstream effects on the timeline eventually allowed the JSA to travel back in time and stop Degaton, sending him back to the point where he shot Zee (All-Star Comics #35).  In the Second, he went to a much more adjacent time point - Pearl Harbor - attempting to intercede at the point America entered the war.  He was ultimately defeated by a new assemblage of costumed vigilantes - The All-Star Squadron - and was again sent back to 1947 (All-Star Squadron #1-3).  In the third, Degaton again shoots Zee and this time goes into the future, stealing nuclear weapons  from Earth-Prime to use in the past, resulting in a nuclear war in the Earth-Prime timeline that destroys civilization.  The combined efforts of the 1940's All-Star Squadron and the 1980's JLA and JSA defeat Degaton and his allies, the Crime Syndicate, once more leaving him in Zee's lab in 1947 (Justice League of America #207-209, All-Star Squadron #14-15),