In the aftermath of 9/11, a lot of federal money was made available for the reconstruction of all the stuff that was destroyed. However, it was only usable for things in the Ground Zero area. So to maximize the utility of all this money, the Port Authority created an insane train station dressed up to the nines to soak up $4B of free federal cash. They also lumped a bunch of other unrelated things into the station that raised the sticker price but would still be covered by the feds.

For what it's worth, this station was also at one point supposed to serve a LIRR extension from Atlantic Terminal to WTC, but kind of died after Pataki could not convince the feds that this was a reconstruction project and he left office. The project was never downsized in scope to match the new reality.