Clay and Tara both went to prison at the end of Season 5 and they are still there at the start of Season 6. Unfortunately, Clay is turning on the club in exchange for not being put into general population.
Fortunately, Tara gets out of jail pretty quickly (though she still has a trial). However, she's leaving Jax and making Wendy the boys' legal guardian if anything should happen to her. Ruh roh.