War
Lyra wasn't the type to hold a grudge. It simply wasn't in her.
People did horrible things all the time. Sometimes, without even knowing it. That didn't mean they were bad, just misguided. Everything happened for a reason. Who was she to judge what she didn't understand? Something that looked horrible and heinous from a bystander's viewpoint could be noble and well-meaning to the person doing it. If she jumped to conclusions without getting the full story, someone could end up getting hurt for no reason. It was better to just go through life with a sunny outlook on things, not sweating the small stuff. If an individual did something she didn't agree with, then she would take the time to understand their point of view, and move on. That's what she did with Silver.
Unfortunately, Team Rocket was a different story entirely.
Truth be told, Lyra wanted to understand them. But no matter how hard she tried, it was impossible for her to see their actions as anything other than horrible and selfish. She couldn't wrap her mind around why they treated Pokemon like mere tools to be used, discarded when they were no longer of any use. Perhaps it was because of the bond she shared with her team. Each time she caught a new member, Lyra was sure to ask them whether they wanted to fight for her. If they said no, then the girl would be more than happy to release them. Team Rocket didn't give their Pokemon that luxury. Once one was captured, it was essentially dooming the poor creature to a life of slavery.
Pokemon loved humans. It was why they were willing to fight so hard for their trainers, despite whatever pain it may bring them. In return, it was only natural that their master would care for them to the best of their ability. The partnership allowed both to grow together, as a team. But, for some reason, Team Rocket didn't understand that. Pokemon were objects in their eyes. And nothing Lyra said or did could change that. All she could do was try to stop them before they did any more damage.
She never intended to get involved in the fiasco at Slowpoke Well. But Kurt was so adamant about stopping them, and she didn't want him to run off alone when he had a young girl in his care. So, reluctantly, she followed him. And it was a good thing that she did, because he ended up hurting himself in the process, leaving her to take care of the villainous team alone. Sweet little Lyra would have to play the hero instead of the damsel this time around. The irony was not lost on her.
What she saw in the well was horrifying. It was her first real look at how brutal human beings could be to their beloved partners, and it changed her. After that day, she still tried to understand people who didn't agree with her, but with Team Rocket she was at a complete loss.
For the first time in her life, Lyra felt true hatred for other people. They were committing crimes that were a complete violation of the bond between human beings and Pokemon. She wanted to do anything in her power to stop them before they caused any more harm.
But, at the same time, it also gave her hope. Because she could stop them. She had the power now, with her beloved team of Pokemon supporting her at every turn. With them, Lyra was able to drive Team Rocket off in Slowpoke Well, despite the fact that she was utterly terrified of the man named Proton. She didn't have to be the damsel anymore; she could play her part in this fight, and play it well.
On that day, Lyra declared war on Team Rocket. Because even a girl like her had the right to fight back against what she thought was wrong.