Will not start, Anti-Theft

My wife had the car running from the remote starter. She then went through the passenger side door to put the key in the ignition. When she turned the key, the car immediately shut off. Now it won't start. When I turn the key part way all the panels come on. But when I go to start the car, everything shuts off except the check engine light. I replaced the battery just to see if that would help but it didn't. Still had the factory battery so I figured it wouldn't hurt to have a new one anyway. How can I fix this? Thank you!