Pull over and charge system message keeps appearing?

You cannot bypass this warning; it is telling you there is something wrong with the hybrid battery. Let's do a CAN scan to confirm the issue, you can get a CAN scanner (Controller Area Network) which will work on most cars from Amazon.

Here is a video to show you how:

https://youtu.be/u-4syLc-ifQ

Please go over these guides and get back to us.

I have an OBD 2 scanner, will this work?

An OBD scanner is limited to some codes. The CAN scan will go into the hybrid systems and the entire car. I don't think an OBD scanner will get us the information we need if you have the scanner plug it in to see what it says.