In 2633, the Neo-Salamander Force, led by their mysterious leader Chief Salamander, travels back to 1973 to eliminate the "Contra" Forces while the Earth Defenses are still primitive. They set up base on the ruins of the Shizuoka Temple at the Yucatán Peninsula in Central America. Bill Rizer and Genbei Yagyu, two members of the present day Contra team, are deployed by Galactic President to travel back in time to stop them. Chief Salamander, however, is nowhere to found. (Sadly, the plot actually makes this much sense.)