Story

Throughout the Portal series, you take on the role of Chell, a young woman trapped within the Aperture Science complex. Chell is forced to solve tests of varying difficulty in chambers designed by an AI-gone-rogue named GLaDOS. During the early stages of the games, Chell is granted access to the Handheld Portal Device (commonly referred to as the Portal Gun), a piece of equipment developed by Aperture Science that allows Chell to create portals that are large enough for her to travel through. These portals act as gates between each other, allowing Chell to quickly traverse areas or reach normally unreachable places.

Portal
Portal has two distinct parts, the test chambers and the escape.

Act 1: The Test Chambers
The game begins with Chell awakening in a Relaxation Vault, where she is briefed by the voice of GLaDOS coming from speakers, before being released through a portal. The player is introduced to the testing process and mechanics, shortly thereafter obtaining the Handheld Portal Gun. As Chell makes her way through test chambers it becomes clear Motivating Chell with the promise of Cake at the end of the testing, Chell is put through tests of increasing complexity.

Portal: Still Alive
Portal: Still Alive is a Xbox 360 Live Arcade port of Portal, containing additional content in the form of new advanced chambers, inspired by Portal: The Flash version, with no additional story material.

Portal 2: Lab Rat
The Lab Rat comic bridges the gap between Portal and Portal 2, which introduces us to Doug Rattmann, a scientist at Aperture Science who survived the Neurotoxin after GLaDOS' first activation at the Bring Your Daughter to Work Day, which made her self-aware and initiated a lockdown on the facility, and killed most of the scientists with neurotoxin.

Part 1
Part 1 follows Doug Rattmann as he is tracking Chell through the Enrichment Center. He is having a monologue about reality and how the mind sees it, and is shown to be psychotic, forced to take ziaprazidone [sic] to curb the effects of his schizophrenia. Through the story, he carries a Companion Cube that he hears talking to him and giving him advice. The main story is also intersected with flashbacks of the period during which GLaDOS was still being built, showing Rattmann's involvement in the project.

Soon after discovering Chell, it appears he has not taken his medication for a while, and he takes his two final pills, against the Companion Cube's advice not to take them. A first flashback is shown, with a younger Rattmann overhearing two colleagues saying they put cameras in the cameras, something that an unidentified person is not to suspect. While he runs through the facility and makes another mural, Chell reaches Test Chamber 19, and finally GLaDOS' chamber, where she destroys her.

Then another flashback set in GLaDOS' chamber is shown. There Rattmann is seen working with his colleague Henry, who compares their breakthrough with GLaDOS to Einstein discovering relativity and NASA reaching the Moon. Rattmann expresses his doubts about GLaDOS' reliability, since she always attempts to kill everyone when being powered.

Back to reality, Rattmann reaches for the surface, where he thinks Chell is. When he finds her, the Party Escort Bot is dragging her back into the facility.

Then a third flashback has Henry showing Rattmann the newly designed Morality Core, which is supposed to dampen GLaDOS' urge to kill.

Again back to reality, the Cube tells Rattmann to run away while he is outside, but feeling he is responsible for the whole mess, he prefers to get back inside, and save her.

Part 2
Part 2 opens with Doug Rattmann traversing the innards of the facility. The Companion Cube informs him that the anti-psychotic he took in Part 1 is starting to work, as the Cube slowly fades to silence. Doug finds Chell in her Cryo-Chamber in the Relaxation Center, where the Party Escort Bot has placed her. He decides to try to save her by getting to Cryo-Control, but the Sentry Turrets block his way. Finding a panel in the wall, he quickly realizes that GLaDOS' destruction blew the main power grid, and that all the Cryo-Chambers have gone offline as a result, including Chell's. Doug then attempts to run past the Turrets but is struck down.

Time for another flashback, this time set after GLaDOS has flooded the Enrichment Center with her neurotoxin. Rattmann, apparently the only survivor, is taunted by GLaDOS about his schizophrenia as he escapes from the main testing facility. While GLaDOS continues to taunt and manipulate him, Rattmann manages to reach the file room where he finds Chell's file, declaring that she's "the one", then puts her on top of the Test Subject list.

Back to the present, Rattmann is lying on the floor, wounded by the Turrets, reaches out to his Companion Cube but loses consciousness.

Another flashback begins, involving Henry having a conversation with GLaDOS. During the conversation, she tells him she has lost all interest in killing since she was fitted with a Morality Core and that she would like to perform a recreation of the Schrödinger's cat experiment during "Bring Your Cat to Work Day". She says that, added to the boxes and the cats, she needs a little neurotoxin. Harry, unaware of her malicious intentions, accepts, "as long as it's for science", thus sealing the employees' fate.

Doug regains consciousness, and his schizophrenia has returned. The Cube can talk again and asks about Chell being "the one" and how Doug knew she is, to which he admits it was just a hunch. The Cube then tells Doug to patch Chell's Cryo-Unit in the reserve grid to restart her life support, which works but keeps Chell in an everlasting sleep until she is woken up, "both alive and dead, until someone opens the box".

Exhausted, Rattmann crawls into the bed of a Relaxation Vault, and presumably falls asleep. It was later revealed by Valve that Rattmann was long dead before the events of Portal 2. On the floor, Chell's files scatter on the ground, showing that she should not be tested, as she is abnormally stubborn and never ever gives up. Ever.

Portal 2
Portal 2 was released simultaneously on PC & Mac, Xbox 360 and PS3.

Trivia

 * In order to flesh out the story in Portal 2, Valve originally intended to include an exhibition within the Aperture Science facility, one composed of different dioramas showcasing various aspects of the company and its philosophy. The dioramas were ultimately cut before the final release.