So upon pulling out all my interior I find two orange plugs (one on both sides) under my back seat in my 99 EM1. What is this plug for?

 

It's a connector for the rear Anti Lock Brakes. You will also find a rubber grommet not too far away for the wheel sensor parts of the wiring to go through. The US models did not come with ABS. In Canada it was included probably because we live in the great white north.
The main wire harness was probably shared on the Lx, Si, Sir and other models made in Marysville to save money on assembly costs.

 

ABS=extra weight...

 

saw the same on my old civic.

 

Good to know, it spiked my curiosity. Thanks guys

 

so this is there to easily add abs?

 

Yes you could add ABS, BUT it will not be cheap

List of items needed,
ABS modulator assembly, all brake lines to convert
ABS computer
4 abs wheel speed sensors ( 1 specific for each corner )
2 front driveshafts ( reluctor rings attached to outboard CV joints )
2 rear wheel bearing assemblies ( reluctor rings on bearings )
AND what ever stuff i'm forgetting

Not too difficult to do but it's added weight and not really required if your running REALLY sticky tires. ( My opinion only as I'm shure it's worth it to some people )

 

cool, was just wondering.