After a conversation and some help from Alan, I have been able to start animating the scene were by the Palace of the Soviets cuts off screen - like a cross section. Below are the stages and fist images of this process.
|Two Sided Shader|
By creating a two sided shader it allowed me to create a 3D mask that travels with a transparency projection across my model.
|Cut Out Hole|
By rendering a cube moving at the same speed as the transparency projections it gave me the texture of my building so that I could apply the two sided shader mask to it.
|Transparency Projection Pass|
Above is the transparency pass that creates the cross section effect.
After compositing the 4 layers together I got the above image. That when put in a sequence, creates the below animated Gif.