When you have UNPOLARISED light passing through the first polariser, malus's law does not apply - only 50% of the intensity of the unpolarised light passes through. The 50% of the light that passes through will have light polarised in the direction of that first polariser. As this light enters the second polariser (called the analyser), Malus's law applies (I=Iocos^2(theta)), where theta is the angle between the polariser and the analyser axes, and Io is the intensity of light entering the analyser. Malus's law simply implies that the intensity of POLARISED light passing through a polariser varies by a factor of cos^2(theta) with the angle between the orientation of polarisation of the entering light and the orientation of the polariser axis (theta). Hope this helps!
