Forensic scientist Barry Allen is struck by lightning and doused in chemical products that afford him superhuman speed, which he learns to control with help from Tina McGee, a scientist from S.T.A.R. Labs. Barry's brother, policeman Jay Allen, is murdered by his corrupt ex-partner, Nicholas Pike, the leader of a vicious gang of criminals.

While Barry investigates the murders of several homeless people whose bodies are being stolen from the crime scenes, Tina reconnects with an old friend, Dr. Carl Tanner, who has recently returned to Central City to retrieve Tina's late husband's research on genetic engineering. Barry and Tina learn that Tanner is using the vagrants in his illegal experiments.

Barry's secret identity is uncovered by Megan Lockhart, a private investigator employed by corrupt District Attorney Arthur Simonson, who blackmails Barry into becoming his secret accomplice in his efforts to bring legalized gambling into Central City on behalf of the organized crime.

Master thief Stan Kovacs assembles a team of criminals, which the police believe intend to steal the Mask of Rasputin from the museum of natural history.

Barry attempts to foil the kidnapping of Sofia Tomarquin, daughter of DEA agent Felix Tomarquin, who is scheduled to testify against drug lord Reuben Calderon. However, Calderon's enforcer, Marcos Trachmann, utilizes advanced microscopic devices to control Barry's nervous system and force him to help them kidnap Sofia.

Barry attempts to protect his father, veteran policeman Henry Allen, from Johnny Ray Hix, a dangerous criminal that Henry arrested 15 years prior and who has escaped from prison to enact revenge.

Barry shelters street orphans Terry and Cory Cohan, who have stolen the backpack of a recently murdered journalist, Philip Sullivan, containing Sullivan's research on a highly addictive synthetic drug known as "Blue Paradise", developed by notorious drug designer Beauregarde Lesko.

Garfield stonewalls Barry and Julio's efforts to locate a cloaked figure who is targeting individuals connected to the arrest of notorious anarchist Zacharias, who was later executed... and Garfield was the arresting officer.

In the 1950s, Central City's guardian was Desmond Powell, who fought crime as "The Nightshade". His nemesis, a criminal mastermind known as "The Ghost", is believed to have died after a confrontation, causing a guilt-stricken Powell to retire. However, the Ghost has in fact preserved himself in suspended animation and resurfaces in the 1990s, where he hijacks Central City's power grids and holds the city for ransom, forcing Powell to return to action and join forces with the Flash.

Brian Gideon, a disgruntled biophysicist, learns that STAR Labs is producing weapons of mass destruction based on his research for the United States government and uses a cloaking device to infiltrate STAR Labs and retrieve the weapons, exposing Tina and the project administrator Ruth to a deadly neurotoxin. While attempting to locate both Gideon and a cure, Barry clashes with federal agent Quinn, who is trying to cover up Gideon's--and Quinn's--involvement in the crisis.

Barry and Julio are tipped off that Wayne Contrell, a famous Jazz saxophonist on the death row for the murder of his wife, lounge singer Linda Lake, is innocent, and given 24 hours to find evidence to acquit him.

James Jesse, a schizophrenic serial killer, becomes obsessed with Megan Lockhart, who had been investigating his activities, and attempts to kidnap her, but she is rescued by the Flash. Believing them to be romantically involved, Jesse adopts the identity of the Trickster and begins tormenting the Flash.

Barry becomes plagued with nightmares and then causes the accidental death of the leader of a all-female gang, the Black Rose. A bio-feedback experiment gone awry causes Tina to develop a malevolent personality, and she seizes control of the Black Rose Gang.

Barry crosses paths with Stacy Doubek, the daughter of Nobel prize winning academics, and her young daughter, Lily, who are fleeing Lily's father, mobster Philip Moses, who wants the child as his heir. After the Flash prevents Moses from kidnapping Stacy, Garfield attempts to use her in a sting operation to lure Moses into a trap, but Moses is tipped off by his men and manages to escape with Lily. The Flash chases him to an abandoned airfield and prevents him from leaving Central City, and Moses is arrested while Stacy and Lily are reunited and decide to stay in Central City.

Nicholas Pike is released from prison on a technicality and attempts to use a missile to kill the Flash, instead transporting him 10 years into the future, where Barry's secret identity has been exposed and Pike has conquered the city.

Philanthropist Curtis Bonnahan, son of Derek Bonnahan, a mobster arrested by the Nightshade in the 1960s, becomes a copycat vigilante known as "The Deadly Nightshade", who employs lethal force in his crusade against crime.

Mobster Jimmy Swain employs hitman Leonard Wynters, also known as "Captain Cold" for his weapon of choice, a nuclear-powered freeze ray, to eliminate his competitors and then the Flash.

Barry is cloned by Dr. Jason Brassel, who names the clone "Pollux". Upon learning he has created for the purpose of weaponization, Pollux goes on a rampage and comes into conflict with the Flash, ultimately defeating him.

Sam Scudder, a criminal mastermind who uses mirrors and holograms to commit his crimes, steals an advanced battery from S.T.A.R Labs East Coast division, which is then stolen from him by his partner, Stacia Masters, who flees to Central City and seduces her former classmate Barry into sheltering her at his apartment.

Petty crook Harry Milgrim and his cousin, scientist Roger Braintree, plan to use a subsonic device developed by Braintree, which places people in an induced slumber, to rob Central City. Milgrim fakes his death to infiltrate the police station and steal valuable information, pinning the blame on Barry, who races against time to both prove his innocence and prevent Milgrim and Braintree from conducting a citywide robbery. In the end, he triumphs, with Milgrim and Braintree being arrested, clearing his name.

Barry and Tina befriend Alpha, an android assassin developed by the United States government who refuses to kill, and protect her from another assassin, Omega, send to destroy her.

Barry feels betrayed when the city treats James Jesse as a celebrity ahead of his trial. Jesse later escapes from prison with help from an obsessive fan, Zoey Clark, and becomes the Trickster once again, with Clark as his assistant, Prank. They brainwash the Flash into joining them in wreaking havoc, damaging the Flash's public image.