Okay, let me try.
Boone was the main character from season one. After helping to rescue Da'an from an assasination attempt Da'an offers him a position as a Protector. Boone says no. After all you have to have this CVI which give you great mental abilities but gives you an imperative to do anything to protect the TAelons and put them first.
Enter the resistance headed by Jonathan Doors with Captain Lili Marquette as a main undercover agent. She is a shuttle pilot working for the Taelons. They try to get Boone to join them by telling them they have a doctor on the inside and have been able to alter a CVI so that while having those great mental abilities won't give him the imperative to help the TAelons.
Boone says no, but then after his wife dies he takes up the resistance on the offer. So he becomes one of those protectors working with Sandoval.
He is THE main character of the first season, but dies at the end of it. Liam takes over as the main character.
Liam is Sandoval's biological son. But Sandoval doesn't know about it. In fact there was an episode where Sandoval needed this certain blood factor to save his life but only a close relative could donate it. He doesn't have any close relatives that he knows of. Liam anonymously leaves some of his blood to save Sandoval.
The Synod is the governing body of the Taelons. The leader of the Synod from the first season is killed at the beginning of the second season. Zo'or and Da'an both try to become the next leader of the Synod. Zo'or manages to become the leader.
Just a side note, Zo'or is Da'an's child.
Hope this helps.
