The game's protagonist, who is initially unnamed, begins the game by awakening in a jungle on Titan, completely unaware of who he is. After a short journey he retrieves a holocube which informs him that his name is Conrad B. Hart, an agent for the Galaxia Bureau of Investigation, and that during one of his investigations he discovered a plot to destroy the earth by shape shifting aliens that have disguised themselves as government officials. These shape-shifting aliens can be detected by the use of monoculars that measures molecular density. Upon discovering the aliens, Conrad uploaded a copy of his memory and gave it to his friend Ian before recording the holocube message for himself. As he feared, he was indeed captured and had his memory erased. The holocube message ends with the instruction to travel to New Washington, which is also on Titan, to meet with Ian and retrieve his memories. He eventually meets a wounded stranger who asks him to find his teleporter. After finding and returning his teleporter, the man teleports away but leaves behind an ID card, which Conrad later uses. Conrad then buys an anti-G belt from another stranger in order to jump down a hole that leads to New Washington.

There, he finds Ian being attacked by a pair of corrupt cops. Conrad kills them, and Ian uses a regenerator in order to give Conrad back his memory. Conrad asks Ian what to do in order to return to Earth. Ian says that the ticket price is huge, and the only way would be to be a contestant on the game show Death Tower. Conrad asks if Ian can give him false papers, but Ian tells him that he needs to ask for Jack in the bar. When he gets there, Jack tells him that the cost is 1500 credits. Conrad gets enough credits by getting a work permit and then completing jobs. Jack then gives him the papers, and Conrad enters Death Tower.

Conrad wins the contest. When he returns to Earth, a gang of corrupt cops discover him and try to kill him. As he fends them off and proceeds, he ends up in Paradise Club, which is really the alien's hideout on Earth. Conrad sees three aliens, all but one in disguise, talking about how they have given the humans the ability to produce their needed power, and how millions of their warriors were soon going to be teleported to Earth to destroy mankind. The vent that Conrad is standing on falls, and the undisguised alien has him thrown in the dungeons and his gun taken from him. Soon, a Death Tower terminator opens Conrad's cell and tries to kill him, but he runs off and finds his gun, which he uses to kill the terminator.

Eventually, Conrad finds a teleporter that leads him to the very distant planet Morphs, which is the home of the aliens. There, Conrad finds a human prisoner named Phillip Howard Clark. As Conrad attempts to free him, a Morph shoots Phillip because his door is opened, only to then be killed by Conrad. Just before Phillip dies, he gives Conrad his atomic charge. He eventually finds his diary, which gives him logic information. Soon, Conrad enters the Master Brain area. Once at a certain spot, Conrad hears Phillip's voice tell him to put the atomic charge at the spot and then flee. Conrad does so as Morphs starts shaking and crumbling, and escapes via a spacecraft and gets out of Morphs's atmosphere just as it explodes.

The game then cuts to Conrad making a message in the spacecraft's journal. Conrad is shown entering suspended animation as the last sentence of the message is shown.

Flashback was and still appears to be mistaken as a sequel to Eric Chahi's video game Another World (the game Heart of the Alien was released as Another World's sequel). Although both games do share similarities, the storylines are completely different, and there is no major connection between two characters in Flashback. Flashback is mistaken as a sequel because both games are published by Delphine, Another World also utilizes rotoscoped animation (Flashback's graphics are similar to Another World, but the gameplay backgrounds are digitized hand-done drawings, while the vectors are pre-rendered compared to Another World, which featured real-time polygons all over, though the 3DO port did have digitized hand-painted backgrounds), and the gameplay of Flashback is similar to Another World (however, Flashback featured step-based controls and a heads-up display while Another World lacked both).

The PC version has an extended introductory sequence and more minor cut scenes than the Amiga version, such as when picking up items. In the Amiga version, the user can see these scenes by enabling them (although with few seconds of delay every time the animations load) or by playing the game entirely from the hard drive. The Amiga version also had an option to zoom in on the action whenever Conrad opens fire. Due to criticism of the look, it was removed from all other versions, although an option to play the game zoomed in remained in the PC version. The message that Conrad writes in the ending was also different in this release.

The game was originally released on 3.5" floppy disk for MS-DOS. The re-release on CD-ROM for Sega CD (later adapted to PC CD-ROM, 3DO and CD-i) featured redone pre-rendered cinematic FMVs with audible dialog and sound. The Sega CD version also has voice work for gameplay and CD tracks for each level which were not carried to the other CD-ROM conversions. The Jaguar port has the title screen that these versions have, but the music is different and the game keeps the original cutscenes, being the CG title screen all that it has from the CD releases.

In North America, the Sega Genesis (Mega Drive), Super Nintendo and Sega CD versions featured a Marvel Comics comic book within the manual in order to explain the initial story. The PAL Sega Mega Drive and Super Nintendo releases (there was no PAL Mega CD version) omitted the comic and instead featured a textual prologue. The Super Nintendo port featured some minor censorship due to Nintendo's content guidelines at the time. Changes included New Washington's bar becoming a cafe and Death Tower being renamed Cyber Tower, while the enemy mutants (who had natural skin colors in other versions) were recolored green.

A two-track CD soundtrack was released featuring music inspired by the game, but not directly from it.

The Mega Drive version became a bestseller. In 1994, Mega placed the game at number eight in their list of top Mega Drive games of all time.MegaTech magazine conceded that although there were "five big levels", finishing the game did not take very long.

It was listed in the Guinness World Records as the best-selling French game of all time. Retrospectively, Wirtualna Polska ranked it as the 17th best Amiga game and the Polish edition of CHIP ranked it as the tenth best Amiga game.

A sequel titled Fade to Black was produced by Delphine Software International in 1995 for the PC and PlayStation. A full polygonal 3D game, it resulted in more slow-paced gameplay and lack of platforming comparing with Flashback, generating mixed reviews from critics who felt that it was too different from the original concept of the series.

A third game in the series, Flashback Legends, was in development by both Delphine Software International and Adeline Software International for a planned released in 2003, but was cancelled when the company went bankrupt and ceased operations at the end of 2002.

In early 2013, a game titled Flashback Origins was rumoured to be in development, with the French website Gameblog stating that €300,000 of government funding had been granted to Cuisset's VectorCell in 2011. An image that looks like a screenshot was anonymously posted to Gameblog, but as of January 2013 it is not known whether it was taken from a sequel, a remake, or is a piece of fan art.

REminiscence, a game engine recreation, was created by Gregory Montoir (cyx). The engine is available for Amiga OS4, Dreamcast, GP2X, iPhone, Linux, Microsoft Windows, Mac OS X, Maemo, MorphOS, Nintendo DS, Wii, Palm OS, PlayStation 2, PlayStation Portable, Sega Saturn and Windows CE. There is also one for the Xbox 360 by MagicSeb. A port for Symbian and Maemo 5 by Ronen K is available.OnEscapee was originally developed as an Amiga CD title, and has since been released as PC freeware. The game contains many similarities to both the Flashback style of gameplay and concept.