The second season introduces the League of American Nationalists (Loan) and they soon create a plan to kidnap and rape Gemma to send a message to SAMCRO. Since Jax pieced together that Donna’s death was indeed the doing of Clay, he begins to question every move that Clay makes. Specifically when a vote is called around the table on important business dealing with the future of the club. A car bomb is placed within TM (SAMCRO’s headquarters) and blown up which brings additional heat from government organizations since certain organizations must be called when explosions are involved. Season 2 truly tests the relationship of Jax and Clay through a series of events dealing with LOAN, without the motivation from Gemma’s rape since she has been kept it a secret because she feels it would be better for the club if their judgment would not be clouded by such an event. It would only be until the club is almost at a breaking point with Jax proposing his resignation of VP that Gemma tells them what had happened to her. This of course fuels Jax to find Weston (member of LOAN) and murder him within the bathroom of the tattoo parlor he was at, this was an important point in Jax’s character arch for it was one of the first times he murdered an individual while Weston’s son was at the tattoo parlor with Weston. This illuminates his willingness to murder those who oppose him and his plans for the Sons of Anarchy.
Gemma restarts her cycle of trouble by following Zobelle’s daughter who was involved in her rape by luring Gemma into her van. After following Zobelle’s daughter for some time, Gemma finds Agent Stahl (ATF agent) with a murdered IRA member. Stahl hides until Gemma enters the building after Zobelle’s daughter and shoots her. Only then does Agent Stahl reveal herself, claiming Gemma murdered both the IRA member and Zobelle’s daughter. Gemma runs off with Chief Unser of Charming Country Police Department and the IRA finds out of the murder after Stahl communicates what happened over her police radio. Cameron then breaks into Jax’s home and stabs a club member to kidnap Jax’s newborn son which he does successfully only leaving Tara behind alive. Cameron travels to a nearby dock where he finds a boat to escape on. Jax’s emotionally state is then questioned season as he collapses on the dock in which Cameron has left with his son, this brings to question his allegiance with the Sons of Anarchy and his role in his family’s life.
Season three opens with Gemma arriving at her father’s home who suffers from dementia. She must put him in an assisted living home after murdering his helper after she finds out that Gemma is wanted for murder. After checking her father into a nursing home Gemma becomes distraught with emotion, suddenly deciding she needs to see her grandson who had been kidnapped. She did not know he had been kidnapped but soon finds out after driving back to Charming, leaving her hiding place from the murder charge allegations. Upon finding out her grandson has been kidnapped she collapses from heart problems and must be brought to the hospital. All the while, Jax’s son is transported to Belfast and the IRA Council must make a decision of what to do with the child. After those residing in Belfast attempt to thwart Jax’s search for his son he eventually gets the Sons smuggled to Belfast to find his son after questioning the IRA’s willingness to help him. Samcro slowly realizes that the charters from Belfast were helping them hide Jax’s son which is why their president is thrown off of a building by Clay for betraying one of the original Redwood 9. While a majority of SAMCRO is in Belfast Tara is kidnapped with her boss and she continues to fight against her captors while the club members remaining in Charming attempt to find her. Later Stahl arrives at TM to arrest SAMCRO which she does, their transport is stopped by Chief Unser and the club murders Agent Stahl and her colleagues which is caused by Jax realizing her under the table work ethic within the ATF agency. Tara then finds the manuscript Jax’s father had written and she begins to piece together Clay’s murder of Jax’s father.
Clay dives deep into the role as an anti-hero during this season as his perception of an individual to the audience becomes clouded with the actions in which he has decided to pursue. By this point Jax has almost finished his father’s manuscript, its effects showing through to the audience as his decisions are augmented into a different direction. These ideas are revealed with a dialogue between Jax Teller and the in which he shares his findings from the manuscript.