The Phazon Tank is really another form of the Energy Tank. However, if the Phazon tank is depleted, you exit Hyper Mode. But if it gets overfilled, Phazon tentacles will appear from the sides of the screen, and if they touch, you get a Game Over with a cutscene of Samus getting corrupted and turning into a "Dark Samus".
In the final part of the game when you are on Phaaze, your suit and you reach Terminal Corruption. This will trigger cutscenes and forces you to vent your Energy Tanks. Like in normal Hyper Mode, you die if your Phazon Meter gets too filled, but unlike before, you can't drain it yourself. You will collect Anti-Phazon Units, the opposite of Energy Units or Phazon Units. The color coding is the same as normal units.
The other way to vent Phazon fron your suit is to get near a Phazon Puffer (Native only to Phaaze), but don't hang around too long, as they will explode and cause your meter to fill up more then it was drained. The last way to get rid of excess phazon, and in case you didn't notice, Phazon is bad very, very bad at this point, is to drain your energy into a (I forgot, but it looks EXACTLY the same, color excluded, as an Inglet found on Dark Aerher in Echoes).