(Abstract Algorithm's and Kevin Reid's answers are good, and only one thing is missing: some actual Three.js code.)
You basically need to calculate where each point of the original sphere will be mapped to after it flattens out into a plane. This data is an attribute of the shader: a piece of data attached to each vertex that differs from vertex to vertex of the geometry. Then, to animate the transition from the original position to the end position, in your animation loop you will need to update the amount of time that has passed. This data is a uniform of the shader: a piece of data that remains constant for all vertices during each frame of the animation, but may change from one frame to the next. Finally, there exists a convenient function called "mix" that will linearly interpolate between the original position and the end/goal position of each vertex.
I've written two examples for you: the first just "flattens" a sphere, sending the point (x,y,z) to the point (x,0,z).
http://stemkoski.github.io/Three.js/Shader-Attributes.html
The second example follows Abstract Algorithm's suggestion in the comments: "unwrapping the sphere's vertices back on plane surface, like inverse sphere UV mapping." In this example, we can easily calculate the ending position from the UV coordinates, and so we actually don't need attributes in this case.
http://stemkoski.github.io/Three.js/Sphere-Unwrapping.html
Hope this helps!