Music theory is a vast topic. Wikipedia is the best place to learn music theory as per my experience. Having someone who can help in guiding you on what to learn next will be a better option in case you are starting new. I started going through Wikipedia and finding it very interesting. Most of the things are mathematics what I feel. As there are lots of scale and all the scales can be played in 12 different keys, things starts to become more complex. I have been using an Android app called Music Companion during the course of my learning and that is helping me a lot in understanding Scales, what chords to play in each scale, Circle of Fifths for each scale etc. It also has a built in metronome with very nice timing and chords can be played along with Metronome beat as accompaniment. You too can try it.
The app is available here: