Macbook's keyboard and trackpad not working

[Manch]

I recently had a big problem with the partitions on my Macbook Air. I still don't understand what happened but basically I opened my mac and it had frozen on the login screen. I tried moving the mouse and it was unresponsive. I thought it had crashed or something so I held down the power button to perform a force restart. I had setup a windows partition on my mac using bootcamp so the mac booted into windows. I shut it down and held down the option key when powering on to selection my OS X start up disk. The disk selection screen did not even come up and it booted straight into windows. Other key combinations such as CMD + R or CMD + OPTION + R did not work either. I couldn't find any information online about my problem and decide to plug a windows keyboard in my Macbook Air. Miraculously this worked and I was able to hold down the windows key + R during boot to enter recovery mode. When I did this, a screen came up with an Apple mouse, suggesting me to power it on. Of course I didn't have any mouse connected and didn't think I would need to connect one as it is a laptop. My trackpad wasn't working so I went and grabbed an external mouse to plug in and it worked.

The problem now is that the mac will only function with the external keyboard and mouse. The built in keyboard and trackpad simple don't work anymore. Whenever I try booting the Macbook Air without an external keyboard or mouse plugged in, I get the same window suggesting my to power on an Apple mouse and keyboard. It seems like a driver related issue but I really have no idea.

I have already tried running internet recovery mode and it has not fixed the problem.

Any help would be greatly appreciated.