Kurt Sutter has taken to Twitter to answer questions from fans about Sons of Anarchy. He talks about Jax Teller's final choice, regarding his sons, and why it took such a long time for him to turn on Gemma (Katey Sagal) and more.
For most of the show, Jax kept a detailed set of journals, where he wrote his thoughts down. He was meaning to give these entries to his children, Abel and Thomas. He wanted them to understand the decisions, the choices, that he had made.
In the final season, he burned them. He informed his ex, Wendy, that he wanted his boys to know nothing about the outlaw life. He settled the debts of his club, and gave up his life.