Well, you see, all the Creators wanted the cure including thomas and teresa and also Aris too. They believed it that if they can track the killzone which is the brain and find the pattern so they can create a blueprint and find the cure. But then when thomas got his memories back, he understood that what he did was wrong and well he didnt change back but he was going on the Gladers side.
He knew that he will fight them becuase now they were killing people and he and teresa were not ready to buy it. They put themselves in the trials becuase they knew it had to end some day. They cannot keep it going and they had to find the cure, but thomas knew that now there was no cure.
Hope i helped......
:)