Season 2 ends with a massive timequake rocking the Legends' ship, which forces them to break the one cardinal rule of time travel in order to fix the problem. But if they are able to destroy the spear, they will face the ultimate consequence.
After obtaining the Spear of Destiny, the Legion of Doom rewrites reality, leaving the Legends changed, perhaps forever. The Legends' and the world's hopes rest with Rory, but being the "hero" is not easy for him. Meanwhile, tension mounts within the Legion of Doom and the reason why the Spear of Destiny needs to be destroyed is revealed.
The Legends devise a plan to retrieve the last remaining fragments of the Spear of Destiny from the Legion of Doom when they find themselves in France at the height of World War I and faced with the knowledge that they must destroy the mystical object. They enlist the help of a soldier named John Ronald Reuel Tolkin and learn that the Spear is leading them into the heart of the war. Meanwhile, the team must all resist the temptation of the Spear; and a former teammate returns.
The Legends track Commander Steel to NASA headquarters in 1970 and learn where Nate's grandfather hid the last fragment of the Spear of Destiny. They also notice a time aberration during the Apollo 13 mission and believe the Legion of Doom might be involved. As the Legends journey into space to intercept Apollo 13, the Waverider suffers massive internal damage and Ray's life is left in jeopardy when he is stranded on the moon.
Rip is captured and forces the Waverider to crash, which strands the Legends seventy million years in the past. Ray leads Amaya and Nate to recover a vital piece of the ship. Meanwhile, in an effort to get the "good" Rip back, Rory suggests they enter Rip's mind, but what Sara and Jax discover in his subconscious is not pleasant and they must fight evil versions of themselves; and Nate and Amaya continue to get closer, but it could cause serious ramifications.
The Legends travel to the winter of 1776 to protect George Washington and the American Revolutionary War. Unfortunately, things don't go as planned, and Sara sends out Nate and Amaya to help. Meanwhile, Jax and Stein, who are busy protecting the incapacitated Waverider from their new enemy, are forced to step into roles for which they feel unprepared.
The Legends try to rescue Rip, but first must focus on locating the Spear of Destiny. Stein thinks he has the perfect person to help but knows involving her will be risky. Meanwhile, Malcom Merlyn and Damien Darhk realize that Thawne is pitting them against each other.
Damien Darhk and Malcolm Merlyn try to capture Rip Hunter in 1967 and create an Aberration big enough to draw the attention of the Legends. However, when the team arrives they discover that Rip has no memories of his past due to "time drift" and is just a graduate film student. After trying to convince Rip of who he was, they discover that he possesses an incredibly powerful artifact known as the Spear of Destiny, which the Legion of Doom is after.
The Legends travel to 1927 Chicago and quickly realize they have been set up by Eobard Thawne, Damien Darhk and the newest member of the Legion of Doom, Malcolm Merlyn. While everyone is trying to fix what they think is the mission, Jax encourages a reluctant Stein to share his secret with the other Legends. But Stein is taken captive and Sara must decide whether to stop the Legion of Doom or save Stein. Meanwhile, Rory gets an unexpected visitor and isn't sure how to handle it.
A superhero crossover event continues with the Legends, the Flash Supergirl and Green Arrow working together to defeat the alien Dominators once and for all. Meanwhile, Stein figures out how the team can terminate the Dominators, but he's distracted by the aberration he realizes he created in 1987.
The Legends travel to the Old West and learn Jonah Hex is in trouble with his arch-nemesis Quentin Turnbull, who wants to conquer the West and make it his own lawless territory. Meanwhile, Rory is ecstatic to be in the Wild West, but Sara makes Amaya work with him to keep him on task, which is easier said than done.
The Legends trace a timequake to President Reagan's White House and are shocked to discover their old enemy Damien Darhk is now a Senior Adviser to Reagan. While the team tries to uncover what Darhk is up to, Sara struggles with whether to seek revenge or help with the team's larger mission. Elsewhere, Stein tries to prevent his younger self from creating an even bigger time aberration.
The Legends discover a time aberration in 1863 and must fight for survival during the Civil War with Confederate soldiers who have been turned into zombies. With the Civil War outcome hanging in the balance, Jax participates in a daring mission by going to a slave plantation with Amaya. Meanwhile, Sara begins to feel the burden of the decisions she has to make as the leader; and Ray struggles to find his purpose on the team.
Nate is shocked to learn he has powers and accidentally lands himself and Ray in Feudal Japan. Sara, Vixen and Rory agree to find Nate and help him master his powers so he can defend a Japanese village from the Shogun and an army of samurai warriors. Meanwhile, Jax and Stein stay back to help repair the ship and find a secret compartment but decide not to tell the rest of the team what they learn.
The Legends travel to Nazi-occupied Paris and are surrounded by the Justice Society of America. They discover a time aberration that threatens the JSA, but the JSA doesn't want their help. Meanwhile, Nate tries to prove he should be part of the team.
Season 2 begins with Dr. Nate Heywood, an unconventional historian, making a shocking discovery. Nate then seeks out Oliver Queen for help to find the scattered Legends. Once reunited, they try to protect Albert Einstein from being kidnapped before the Nazis destroy New York City with a nuclear bomb. Meanwhile, Ray notices that Sara has a mission of her own, which leads them both to face her nemesis, Damien Darhk.