conceptually, if you are doing this on a cell by cell basis, you could use RasterToNumpyArray to convert the rasters to arrays...then 'flatten' the arrays so they essentially become X, Y pairs, then you can use matplotlib to do the scatter plot
from matplotlib import pyplot as plt
xs = [1,3,2,5,6,4]
ys = [3,2,1,5,3,2]
plt.scatter(xs, ys)
main_title ="My first graph"
plt.title(main_title, loc='center') #loc is either left, right or center
plt.minorticks_on()
plt.tick_params(which='major', direction='in', length=6, width=2)
plt.tick_params(which='minor', direction='in', length=4, width=2)
plt.show()
