When I downloaded the Metamask Chrome extension it asked me for my seed phrase. Since I'd never downloaded it on my computer before, I figured it was legitimate and that it was trying to authenticate my account. I really think this is where I messed up.
OMG... if you give the seed to any legitimate-looking request, what you think is the use of the hardware wallet, really?!
OK, so since your wallet is now empty, please start with resetting the wallet to a completely new seed, write that down for backup and ever use it again
only when your hardware wallet will ever stop working.
Keep the new seed safe (offline!) and remove the old seed from all the places you've stored it (so you don't get confused in 5 years which one was the correct seed).
And from now on, anything you want to do with crypto, do through the hardware wallet. If Metamask cannot handle the hardware wallet, use MEW with the hardware wallet.
And, sorry if it sounds harsh, but learn to ask here when you are not sure
before doing something stupid, not after doing that.