In Star City 2016, Eobard and Damien recruit Malcolm just hours after the 2016 Damien was killed by Oliver. Martin reconcile, while the Legion restores Rip's memories, albeit with "adjustments". In New Jersey, 1776, Rip shoots George Washington.

During the New York attack, Rip recovered the Spear of Destiny from the Waverider and used the time drive to escape. In the present, the team learns about the spear and arrives in Los Angeles, 1967, when they confront Darhk and Malcolm attempting to kidnap Rip, who has no memories of his previous adventures and is training with George Lucas. Both parties escape; and Rip is arrested by the police. The team abducts him from custody and takes him to the Waverider. Nate and Ray are revealed to have lost their specialties and powers since the aberration caused Lucas to quit filmmaking. While Nate, Amaya and Ray meet Lucas to dissuade him, the others learn that Lucas has a fragment of the spear. Darhk and Malcolm overpower Amaya's party and forces them to search for the fragment in a dumpster. The others arrive and a battle ensues, during which they recover the fragment and the Medallion; but Rip is abducted by Eobard, whose partners intend to torture him to find the other fragments. Lucas returns to filmmaking; and the team vows to rescue Rip. Meanwhile, Mick tells Stein about his hallucinations, which the latter eventually interprets are emotional, not neural.

Eobard, Darhk and Malcolm Merlyn arrive in Chicago, 1927, and ally with Al Capone. Learning of the aberration, the Legends arrive and manage to keep Capone from murdering Eliot Ness. Ness is critically injured, so the team decides to obtain vital information on Capone's operation to secure history. Meanwhile, Mick begins having hallucinations of Snart, who belittles him for acting like his teammates. Sara and Martin are abducted by Eobard during their infiltration and raid on Capone's club. Malcolm offers Sara a chance to change her past in return for the amulet she took from Darhk in 1987, but she refuses. The team rescues the captives, but "Martin" turns out to be a disguised Eobard, who searches the Waverider at super-speed for the amulet while Malcolm attacks the ship directly. Eobard barely escapes revenge at Amaya's hand, but Sara surrenders the amulet for Martin's safety. The Legends succeed in correcting the timeline. Eobard later shows his partners that the completed amulet projects a holographic map that can locate the Spear of Destiny, which is able to "rewrite reality itself". They must next locate Rip Hunter, who is revealed to be working as a movie director in 1967 Los Angeles.

Nate, Mick, Amaya, Felicity and Cisco travel back to the first Dominator invasion of Earth in Oregon, 1951. The Legends successfully capture a Dominator for information, but are themselves captured by Federal agents. While in custody, they learn from the Dominator that the aliens arrived to assess the threat humanity posed now that metahumans have appeared. Felicity and Cisco rescue the Legends and help set the Dominator free. Meanwhile in Central City 2016, the team learns that the Dominators know about Barry's manipulation of the timeline, and that they demand his surrender in exchange for peace. After the Legends return, the team discovers that the Dominators' weapon is a bomb that will kill all metahumans on Earth, with millions of collateral human casualties. The teams dissuade Barry from surrendering, with Cisco reconciling with him. They manage to destroy the bomb and force the Dominators to retreat using pain-inflicting nanotechnology. Cisco gives Supergirl a device to travel between their universes. Martin convinces Jefferson not to tell the others that his daughter, Lily, is an aberration of the timeline.

This episode concludes a crossover that began on The Flash season 3 episode 8 and continued on Arrow season 5 episode 8.

The team learns of an aberration in Colorado, 1874, where they save Jonah Hex from execution. He reveals that he is fighting an outlaw boss named Quentin Turnbull. Nate reveals that the aberration is Turnbull leading the Western US in its secession to form the "Turnbull Country". The team learns that Turnbull is extracting dwarf star, which Ray used for his A.T.O.M. suit, and that Turnbull is planning to destroy a critical railway connecting the Eastern US to the West, stopping the US Army from marching toward the West. While Sara and Jonah engage Turnbull, Mick and Amaya destroy the mine, and Nate uses his powers to stop the train. Instead of killing Turnbull, Jonah decides to deliver him to the authorities. With the dwarf star taken, Ray plans to rebuild his suit, and shows Nate the suit he has made for the latter. Amaya decides to teach Mick to control his anger. Martin and Jefferson deduce that due to the former's interaction with his past self, he may have married another woman. Sara tells the team that they need to return to 2016 to help their friends.

In 1987, Eobard Thawne offers Damien Darhk an alliance, which Darhk declines. Aboard the Waverider, Nate discovers an aberration in 1987 involving the INF treaty signing. The team infiltrates the White House as tourists and find Darhk there as one of the treaty negotiators. Sara again attempts to kill him, which alerts White House security and forces the team to make a very public escape. They soon learn that Darhk is making his own secret deal with the KGB. Returning to the White House during a State dinner, they discover him making an exchange with KGB agents for a box with an unknown item. The team defeat Darhk's men and the Russians. Sara confronts Darhk, but spares his life. Instead, she reveals his future to torture him: his master plan's failure, his wife's murder, and his own eventual death. Eobard whisks Darhk away, but not before Sara steals the box from him. She realizes the team is up against a time-travelling speedster. Unnerved by Sara's revelation, Darhk insists on teaming up with Eobard, and the two enter the time stream.

The team learns of a time pirate stranded in the American Civil War. Upon arriving, they encounter a black man, Henry Scott, being chased by Confederate soldiers turned into zombies from a virus carried by the pirate. The team defeats the group of zombies, but Henry is killed. Before his death, Henry reveals he is a Union spy assigned to steal Confederate battle plans for General Grant, and asks Jefferson to complete his mission. The team discovers that Mick is infected with the virus and return him to the Waverider, where Ray and Martin ultimately manage to cure him. Sara and Nate go to warn Grant about the zombies, while Jax and Amaya attempt to steal the plans. Jefferson runs afoul of a plantation owner and is locked up. Amaya frees him, along with other black prisoners. They find the plans and burn down the mansion during a zombie attack. Meanwhile, Grant's camp is also attacked by zombies. Sara formulates a successful plan to kill them using Nate's powers. Jax, as Henry Scott, gives the plans to Grant, which will ensure a Union battle victory. A grateful Mick gives Leonard Snart's cold gun to Ray.

Amaya stows away on the Waverider and attacks Mick, believing him responsible for Rex's death. Nate stops her using his newly-developed metahuman ability to convert his body to a steel-like form. Sara convinces Amaya that a rogue time traveller is likey to blame for the murder. An accident during Ray's testing of Nate's abilities throws both men into the time vortex and strands them in 17th century feudal Japan. Nate is found and cared for by Masako Yamashiro, the betrothed of shogun Tokugawa Iemitsu, whose samurai capture Ray. Sara, Amaya and Mick rescue Ray from Tokugawa, who uses the Atom suit against them. They meet up with a recovered Nate, who does not want to leave Masako to Tokugawa's mercy. They defend Masako's village from the samurai, while Ray and Nate defeat Tokugawa by destroying the Atom suit. Nate and Amaya officially join the team. Meanwhile, Jefferson and Stein discover a hidden armory inside the ship and a secret message from Barry Allen from 2056 intended for Rip and forbidden for the crew.

The Justice Society captures the team, believing them to be Nazi spies. Nate reveals that he is the grandson of JSA member Commander Steel. After the JSA is assigned a mission to obtain information on Nazi Captain Baron Krieger, they release the team and strongly advises them to leave 1942. The JSA learns that Krieger was given a serum by Eobard, who wants to make a deal for an amulet in Hitler's possession. Nate soon discovers that the JSA dies on this mission, so the team travels back to rescue them. While the others collect the amulet and fight the Nazis, Krieger uses the serum on himself and turns into a monstrous superhuman. He manages to capture Ray and JSA member Amaya. Ray offers to replicate the formula to save Amaya. The teams then attack the Nazi base, save Ray and Amaya, and take down Krieger. However, hemophiliac Nate is critically injured in the process. Ray saves him by using the modified serum he developed. After the team departs, Eobard appears at the JSA headquarters and stabs Rex Tyler to erase him from the timeline before stealing the amulet. A dying Rex whispers "time traveler" to Amaya.

In 2016, historian Nate Heywood enlists Mayor Oliver Queen's help in locating the Waverider after it was caught in a nuclear blast in 1942. The pair find the sunken ship with only Mick aboard in stasis, who tells them what happened after being revived. Rip's team—Mick, Ray, Sara, Jax, and Martin—traveled through time dealing with "aberrations" in history. They learned that a nuclear bomb would be detonated in New York City in 1942. The team discovered Damien Darhk, working with the Nazis, was behind the attack. Sara attempted to kill Darhk to prevent Laurel's death, but Darhk escaped and launched his sole atomic bomb toward New York from a U-boat. Rip chose to scatter the team throughout time, except for the injured Mick, to save their lives while he intercepted the bomb with the Waverider and saved New York. In the present, Mick and Nate use the Waverider to travel through time and rescue everyone, but fail to find any trace of Rip. After fixing events in 1942 to prevent the Nazis from making a nuclear bomb, the team is confronted by the Justice Society of America (JSA). Meanwhile, Darhk is shown to be working with Eobard Thawne.

Rip returns the team to 2016, unwilling to let them continue with his mission, but they insist on seeing it through. Kendra leaves a message for the team alerting them to Savage's presence in 1944 France, but they are unable to stop him and can rescue only Carter. Savage reveals that the Thanagarians sent three meteors to ancient Egypt. He plans to use Kendra's and Carter's blood to activate the meteors' alien technology and erase time back to 1700 BC, where he will rule. Dr. Stein deduces Savage's method: to conduct the same ritual across three separate time periods, creating a paradox that will facilitate time's destruction. He also concludes that radiation from all three meteors will render Savage mortal, so anyone can kill him. The team breaks up into pairs—Mick and Ray, Sara and Firestorm, and Rip and Carter—and travel to 1958, 1975, and 2021, respectively. All three groups kill Savage. Ray and Firestorm destroy their meteors, and Rip uses the Waverider to send the last meteor into the sun before it explodes and destroys the Earth. Kendra and Carter stay behind in 2016 while the others decide to help Rip protect the timeline. Before they leave 2016, however,Rex Tyler arrives and warns the team of their impending death.