>>38364480Because Zinnia sent her Salamence to traumatize and possibly even murder Ruby and Sapphire back when they were kids (this was actually present in the original R/S chapters, it's just that we've only now learned the mence belonged to her).
She did this because (iirc) she learned they were Rayquaza's chosen ones and she got jelous and decided to try and get rid of them both because her thirsty ass wanted to be the chosen one instead.
Also, she nearly destroyed the world because she was the one who got Team Magma/Aqua to get the primals to fight to begin with (at least in the games). She's also very proud of this.
She ALSO (again at least in the game I don't read the manga) nearly destroyed our world again for a SECOND time by destroying the only possible means they had of getting rid of the meteorite, dooming the world to destruction on the offhand chance that, hypothetically, another random world out there will be destroyed by it, despite having literally NO proof to back it up in the games themselves and being a crazy, raving homeless lunatic to literally everyone yet expected to be taken seriously.
Also (in the games, again) she beats the shit out of a few kids, knocks the protag out hard enough for them to be out an entire day, steals from basically everyone, robs people of all their stones, etc, and is in general just a really really horrible person.
Also in the manga specifically she believed herself to be some kind of savior and was practically demanding Rayquaza to listen to her commands while she's still trying to beat the shit out of his actual chosen ones.
I actually can't think of a single reason why he shouldn't have just killed her
and she still somehow manages to survive this, though at the very least she now has to live with the fact that A: she's been disowned by her god and is considered a monster, and B: her body is so horribly fucked up by it she's actually wheelchair bound so she can't walk anymore. 
