They were first seen accompanying Big Boss in his SEMMEcraft en route to the Martian Embassy. Once a beachhead was established, they proceeded to... not do very much of anything at all, really. When Big Boss needed their help the most, they hung out back in the shuttle, sitting guard over Tony's corpse.
Eventually, after gaining access to the Embassy, Science Team 3 brought Tony's body along, in hopes of finding a Martian Resurrection Chamber. These hopes were dashed when Monkey Master, surprisingly stealthy for a twenty-foot robot, snuck up behind everyone and smushed Tony's corpse but good. The sudden arrival of The Cheese, who kicked everyone out and locked the doors, meant that every single stupid thing that had happened thus far was entirely meaningless.
It is possible that Doug and Matt were killed in the ensuing chaos, as they did not seem to reappear afterwards. Marcus, however, showed up around SEMME HQ from time to time after that.