Everyone was angry at him because he may have just started a war between the Phands and the Confederation.
Junup, the turtle which is the Supreme Justice leader, and Visio-om, a Phand which is the representative of the species that was in the destroyed ship, tried to get Zeke to be found guilty, and to do that they had to convince the council members to find Zeke guilty, they did that but a friend of Zeke, Tamret, hacked the vote so he would be found not guilty.
They discover why everything is happening the way they are, like why the Phandic ship attacked the, why they were recruited and that the "Randoms"(Randomly selected candidates to represent their planets in the confederation) were not randomly selected, and their mission to save the members of the selection committee.
So with the information they learned and the information Dr. Roop gave them, Zeke, the human representatives, Tamret (humanoid alien cat), and Steve (humanoid alien lizard) went save the selection committee which he learned included his dad, in which he thought was dead because of a car accident, but was actually alive and had converted to look like an alien (to convert on the book means to change your appearance to look more like another type of alien).
They rescued everyone and came back to the Confederation.
Junup send Zeke and all the other representatives from all the other planets back to their home planets and Dr. Roop made sure to (secretly) give Zeke an nanite injection to cure his mother. But Zeke's Dad stayed because he broke the law by faking he was another species.