In part one of the two-part season finale, the 11th pilgrimage arrives, though only a few new colonists emerge before the Phoenix Group mercenaries begin an invasion. Kara, Josh's girlfriend, is killed in the fracas by a suicide bomber, and Jim Shannon is injured. Facing possible heavy casualties and cut off from reinforcements, Lt. Washington surrenders Terra Nova to the Phoenix Group. Harsh martial law is imposed, while Commander Taylor and most of the colony's security forces are isolated outside the colony. With Lucas and Mira's assistance, the Phoenix Group begin their mission to strip the new world's resources, destroying the environment in the process; meanwhile, Jim Shannon, Lt. Washington, and other colonists coordinate with Commander Taylor in guerrilla warfare to resist the Phoenix Group. At Boylan's Bar, Josh gets his job back and when he keeps giving drinks to Lucas, Lucas becomes drunk and when Skye shows, he reffers to her as his "sister" out loud and touches her physicaly, angering Josh and he hits him to defend Skye. Skye rushes to Jim and tells him about Josh and Jim rushes to go and help his son. While defending Josh, Jim gets into custody by Lucas, along with Josh. While in custody, Josh talks to his father about how angry he was back in Chicago when Jim punched that cop when they attempted to take Zoe away from the Shannon residence, as he relizes he was doing it to defend his child, just like he did back at the bar to protect him. When Josh gets released, Lucas interogates Jim, but this angers Josh more and than ever, and he shouts at Lucas, saying, "Don't touch him!" which Lucas, of course, ignores. Mira, meanwhile, is sent north on a secret mission to the badlands to retrieve an unknown item. Lt. Washington sacrifices herself to create a diversion that will allow the Shannon family to escape the colony and join Commander Taylor in the jungle. Lucas executes Lt. Washington as Taylor and Jim watch helplessly from the trees.