During the first stage of this battle avoid the charged beams he fires (you should be able to hover over it like you did during the hive queen battles). When he jumps up and hangs in mid- air for a bit head up to him and shoot with the sonic attachment. He will then fire some small electrified mines- just keep running to avoid these. Again, once he starts hanging in mid-air, go up and fire with the sonic blast to damage him. After 4 hits you will be into the second phase of this battle.
During this you and the boss will be on a set of platforms. When he starts to charge up a shot hover over using the path of green spray refills to the coil, then flame it to bring down the dark eco level. This will let you jump to the next set of platforms. On the next set do the same thing only to the lft side of the room (facing the boss) and you will get a cutscene bringing you to the last phase of the battle.
Phase 3 sounds somewhat easier than the first two, i think. He will fire one mine- dodge it and hit him with a sonic shot to knock him into a pile of barrels. They will fall on him, pinning him down for another shot in the face. Do this 3 times in all and the game is finished.