After the defeat of the immortal villain Vandal Savage and the exposure of the corrupt Time Masters, a new threat emerges. Dr. Nate Heywood, an unconventional and charming historian, is thrust into the action. After making a shocking discovery, Nate seeks out Oliver Queen for help in finding the scattered Legends. Once reunited, the Legends continue their new mission to protect the timeline from temporal aberrations – unusual changes to history that spawn potentially catastrophic consequences.

The Legends travel to Nazi-occupied Paris, but find themselves surrounded by the Justice Society of America (AKA JSA.) The Legends force their way into the JSA's mission to intercept and seize a mysterious package. Nate is desperate to prove that he should be part of the team, but he has a secret that he shares with his grandfather Commander Steel that might make it difficult. Meanwhile, Stein has stepped in as the leader with Rip gone, but when decisions aren't being made Sara seems to be the one calling the shots.

Nate is shocked to learn that he has powers but then accidentally lands himself and Ray in Feudal Japan. After Sara convinces their stowaway Amaya, AKA Vixen, that Rory is not a murderer, they all agree to find Nate and help him master his powers in order to defend the Japanese village from the Shogun and his army of samurai warriors. Meanwhile, Jax and Stein stay back to help fix the ship and find a secret compartment but decide not to tell the rest of the team what they learn.

When the Legends discover a time aberration in 1863, they find themselves fighting 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 must participate 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.

When the Legends trace a timequake to President Reagan's White House, they are shocked to discover their old enemy Damien Darhk is now a Senior Adviser to Reagan. As the team works to uncover what Darhk has up his devious sleeve, Sara struggles with the choice of getting revenge or helping with the team's larger mission. Thinking that the JSA members could be of help, Amaya and Nate break into the JSA and are surprised at what they find. Meanwhile, Stein tries to prevent his younger self from creating an even bigger time Aberration.

The Legends are still reeling from the news that their time travel-nemesis is a speedster when they are alerted to an Aberration in the Old West. When the Legends arrive they find their old friend Jonah Hex in trouble with his arch-nemesis, Quentin Turnbull. The team soon discovers that they need to stop Turnbull and his gang from conquering the West and branding it his own lawless territory. To Hex's surprise, Sara is in charge and dispatches the team. Meanwhile, Nate, Ray and Jax try to infiltrate Turnball's gang, but find themselves in a shootout.

After learning the Dominators' plan for the world, the Legends must work together with The Flash, Supergirl and Green Arrow to kill them once and for all. Meanwhile, Stein figures out, with the help of others, how the team can terminate the Dominators, but is distracted by the aberration he realizes he created in 1987.

When a new Time Aberration is discovered by the Legends, they find themselves headed to 1927 Chicago. The Legends quickly realize that 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 help fix what they think is the mission, Jax encourages a reluctant Stein to share his secret with the other Legends. Meanwhile, Rory gets an unexpected visitor and is not sure how to handle it.

When Damien Darhk and Malcolm Merlyn try to capture Rip Hunter in 1967, they 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 are determined to find and 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, Malcolm Merlyn and Damien Darhk realize that Thawne is pitting them against each other.

When The Legends find a new Time Aberration they learn they must travel to the winter of 1776 to protect George Washington and the American Revolutionary War. Unfortunately, things don't go as planned, forcing Sara to send 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 that they don't think they are prepared for.

The Legends continue their quest to hunt down the Spear of Destiny before the pieces fall into the hands of the Legion of Doom. The Legends discover that pieces of the Spear are each being guarded in different time periods by members of the JSA. Their first stop is the future where they find Dr. Mid-Nite which eventually leads them to the past and King Arthur's Camelot, where Stargirl is protecting her piece of the Spear. In order to protect the Spear shard from the now-evil Rip Hunter, the Legends must join forces with the Knights of the Round Table.

After capturing Rip, he forces the Waverider to crash, leaving the Legends stuck seventy million years in the past. Ray leads Amaya and Nate to recover a vital piece of the ship. 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. Meanwhile, Nate and Amaya continue to get closer, but it could cause serious ramifications.

When the Legends track Commander Steel to NASA Headquarters in 1970, they learn where Nate’s grandfather hid the last fragment of the Spear of Destiny. The team notices a time aberration during the Apollo 13 mission and believes that 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. Meanwhile, tension grows between Rip and Sara as to who is the leader of the team.

The Legends must devise a plan to retrieve the last remaining fragments of the Spear of Destiny from the Legion of Doom. They find themselves in France at the height of World War I faced with the knowledge that they must destroy the mystical object. They enlist the help of a soldier by the name of John Ronald Reuel Tolkien and find that the Spear is leading them into the heart of the war. Meanwhile, the team must all resist the temptation of the Spear, and the return of a former teammate.

After obtaining the Spear of Destiny, the Legion of Doom rewrites reality, leaving the Legends changed, perhaps forever. Frightfully, the Legends' and the world's hopes rest with Rory, but being the "hero" is not easy for him. Meanwhile, there is tension within the Legion of Doom and the reason why the Spear of Destiny needs to be destroyed is revealed.

As the Legends are about to take off for their next destination, a massive timequake rocks the ship. In order to try and fix what has happened, they are forced to break the one cardinal rule of time travel. But if they are able to destroy the spear, they will face the ultimate consequence.