I ended up doing something similar to what Walter Roberson suggested, i.e. using a for loop. Initially, I wanted to get the plots into a subplot, but realized that would be too complicated. The code similar to what I did is below. (Note: I had to do three cases of tau and two cases of M).
for tau = [T, 5*T, 10*T]
% computations of equations for three cases of tau
for M = [M1, M2]
% commutations for two cases of M
% plot of equations
end
end
Once executed the code, I ended up with six individual graphs. Once the code was published to PDF then everything looked alright. Using the for loop shortened my code from 200+ lines to just 30-something lines.