I saw people having problems with this fight, if charging bullets is not possible (which happens, if you enter this level with Early Echoing Caves trick).
You generally complete entire fight in 3 cycles:
1st cycle: you run diagonally (see input display) and make the Clark stand close to the blue thunder
2nd cycle: when Clark is about to fall down, you run towards him so that when he lands, you stand between him and the thunder
3rd cycle: the same
For each cycle make sure to hit him twice at his back.

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