Okay, so I want to go the NCR route.

I entered the fort to get evidence for Regis against the Legion so the Great Khans side with the NCR and I don't have to kill them all.

However, when I did that, Caesar took the Platinum Chip and I can't get it back. I don't want to go into the weather station and use it. When I left the fort they told me "Caesar has permitted you to leave but not with the platinum chip"... So I am like... how am I supposed to proceed in the game.

Unless you don't need the platinum chip with the NCR?

Is this the case?

Assistance? Help? Please?

It won't hurt to go into the bunker, you don't have to do what Caesar wants you to do anyway. Just follow the quests and you'll be fine. You go in the bunker, and you'll come out, talk to Caesar again, then you'll leave and get all your stuff back. Then just play the game on whatever path you choose, you'll get some quests pop up about Caesar but you don't have to do them if you want to side with the NCR, just go with it and you'll be fine!

you do you not need the platinum chip for the NCR playthrough...

Go into bunker, do stuff, go out, tell Caesar "I'm done working with you". He'll flip out, but you'll get the chip back, and you'll be able to do other things.

In addition, if you have a positive rep with the Legion when you tell him "Screw you", then as long as you keep that positive rep (not long if you're going NCR) you'll be able to grab things from a dropbox near Cottonwood.