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Toxic 2 is an amazing free browser-game by Nitrome.
I saw a lot of walkthroughs and instructions for various levels and hidden levels of Toxic 2, including the boss-level (with a giant supercomputer called Mother).
I believe my way to beat the Mother is the simplest and the quickest one. Only 60 sec and it's over and no health points wasted. Check this out! And it's really simple, you don't need to do anything special or extra-tricky and complicated.
Actually, you don't have to follow this video exactly as it is, just understand the basics: a) you have to be quick to place some bombs "inside" Mother's broken shield, before she regenerate it; b) you should jump up to avoid laser; c) you should avoid pieces falling down closer to the end, to avoid health loss.
PS The music used as a background in this video is Aleksey Petin's "trbus", it's taken from a a free web-release, you can check his album here: