Watch the Phrygian: Dom. Over II-V-I online guitar lesson by TrueFire from Jazz Guitar Greatest Hits Vol. 1
Lesson Source: Kenny Wessel's Shades of Jazz
A progression that we see frequently in jazz and other music and all need to learn to negotiate is an II-V-I progression. Some of us have been probably dealing with an II-V-I progression already, but using all scales derived from the same major key. In this section we're going to discuss how to introduce some altered dominant harmony into our playing using a very familiar scale, one that we've probably already been using in our playing. For instance, for a II-V-I progression in the key of G, many of us would use an A dorian mode over the A min 7, the II chord, then use a D mixolydian mode over the D7 chord (V chord) and resolve to a G major/Ionian mode for the G maj7 chord (I chord). This works, and sounds fine, especially if you target chord tones, use good voice leading, play with melodic and rhythmic interest, etc. If you notice, all these scale choices are in the key of G, and none of the scales contain any altered notes... its very diatonic.
If we want to introduce some altered harmony into our playing, then we can use the D Phrygian mode (instead of the D mixolydian, non-altered scale) over the D7 chord! Now we have an altered dominant sound over the V7 chord: b9, #9, 11, b13. Remember, even though there is no major 3rd in the Phrygian mode, it is implied by the chord we are superimposing the scale over - so we hear the dominant harmony and the b3 (or #9) becomes an altered tension. So with the II-V-I progression: A min 7 / D7#9 / G maj7 , we can use the following scale choices. On the A min 7 chord ,we can use an A dorian mode; for the D7#9, we can use a D Phrygian mode (Bb major scale from the 3rd degree); and for the Gmaj7, we can use a G Ionian mode/G major scale. As you see, this is now not all diatonic. We're going from the key of G major, to Bb major and resolving to G major.