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This is the hardest fucking battle I've had in my whole playthrough so far. Remember, we're fighting on water:
* Grounded non-water types' Speed is halved, except for Swift Swimmers
* Ground attacks always fail
* Spikes and Toxic Spikes sink into the water, vanishing
* Dive lasts only one turn
* Activates Swift Swim, Hydration, Torrent
* Aqua Ring restores 1/8 Max HP each turn (from 1/16)
* Grounded Pokemon with Dry Skin and Water Absorb gradually restore HP
* Whirlpool deals 1/6 Max HP damage per turn (from 1/8) and confuses the target
* Water and Electric moves increase base power x1.5
* Fire moves against grounded Pokemon decrease base power x0.5
* Nature Power becomes Whirlpool
* Camouflage changes user's type to Water
* Secret Power may lower speed
>level 80 Kyogre
>>>>>Water and Electric moves increase base power x1.5
>>>>>Grounded non-water types' Speed is halved, except for Swift Swimmers
The speed drop is what kills us. I have to pray for Breloom's quick claw to trigger to spore and seed it. The rest is Greninja stalling with substitute. Thanks to Protean, Fran only can outspeed the Kyogre before she makes a move.
We win in the end, after more tries than I counted.