How would I go about setting up a rotation matrix to rotate a set of points that are all on one plane to be oriented onto another plane? The points lie on some arbitrary plane in R3 formed by the black line, and i would like to rotate them to all be oriented along the xy plane, (0,0,1). What would be the easiest way to do this?

The easiest way would probably be to determine the axis-angle rotation, and then convert that to a rotation matrix. What you do is take the cross product between the plane normal and (0,0,1) to get the rotation axis, and the dot product to get the rotation angle as per the dot-product formula |a||b|cos(θ). You can then reference this page on how to create the rotation matrix. Once you get everything working, a lot of the operations can be optimized, such as the cross-product and dot-product, since you're working with a constant vector (0,0,1).

That seemed to do the trick, thanks.