Between Minds

Between Minds, written by 3theCaptain, is a Half-Life / Portal fan fiction currently being published on http://www.fanfiction.net/s/7466762/1/Between-Minds. The story's chapters alternate between the two games: as Gordon Freeman, Alyx Vance, and Barney Calhoun deal with the aftermath of Half-Life 2: Episode 2, Chell makes another escape attempt from Aperture Science between the ending of Portal 1 and the beginning of Portal 2.

Plot summary
(Spoilers)

Welcome!: Having survived the explosion at the end of Portal 1, Chell awakens in the Aperture Science Relaxation Center covered in injuries. As she slowly heals in stasis, she formulates a plan to escape her room.

Data Points: After Eli's death at the hands of the Advisors at the end of Episode 2, Dr. Kleiner and Dr. Magnusson decide to postpone the expedition to the Borealis until the following morning. Gordon and Alyx doubt the prudency of the change in plans, but change their minds once they see the new plan: overnight, Kleiner and Magnusson patched up an old teleport prototype at White Forest. They intend to transport them instantly to Dr. Mossman's location, which is an old Arctic laboratory called Adlivun Electric. Gordon and Alyx share a brief moment of solemnity over Eli's death before the former disappears into the portal. However, at Adlivun Electric a battalion of Overwatch troops is waiting to ambush him.

Watch for the Lambda: Chell escapes her imprisonment in the Relaxation Center and makes her way through the abandoned facility. It leads her to a lobby she distantly recalls from her childhood, but to her dejection there is no exit. Deciding she can only return to the surface with the help of a portal gun, she jumps down the elevator shaft to the Portal Technology wing. On her way, she bumps into the Oracle Turret, who gives her the enigmatic advice to 'watch for the lambda.'

Uncertainty Principle: Once the teleport prototype at White Forest cools down, the group prepare to send Alyx through as well, unaware of the ambush on the other side. However, before the portal can enter its final sequence there is a catastrophic malfunction. Alyx is shocked, but unharmed. Minutes later, Barney arrives by crash-landing an Advisor pod into the woods, accompanied by a handful of surviving rebels. Alyx decides to send a message to Gordon via the White Forest radio tower; soon after, sentries around the base detect a Combine army preparing to invade.

An Unexpected Party: Having made her way to an Enrichment Sphere, Chell meets a small family of personality spheres who promise to help her get a portal gun. In return for helping them download into the safety of the mainframe, they provide her with one, along with a blank personality sphere equipped with encyclopedic knowledge of Aperture Science. As the information sphere guides Chell through the facility, both are sucked into a rip in space at the Borealis dry dock.

Damage over Time: Alyx and Barney battle the invading Combine army. Seeing how broken up she is over her father's death, Barney tells Alyx to really think about whether she's up for the mission. Before she reaches a conclusion, they meet up in the control room with Uriah, a vortigaunt scientist; Sam, a demolitions expert; and Marcus, a rebel. The five of them reach the conclusion that the army is being directed by the same two Advisors who attacked Eli in the helicopter hangar; their plan is to kill them by detonating an EMP. The base is then flooded by hunters, forcing the group to flee.

Heal over Time: Alyx and the vortigaunts orchestrate a ceasefire by reverse-engineering the Advisor pod Barney crashed, giving everyone enough time to heal themselves and prepare to fly the helicopter to plant the EMP. Alyx discovers the hunters attacked from inside White Forest. One of the people Barney rescued breaks down, and the next we see of him he is hiding a mysterious sheet of paper.

Area of Effect: After a helicopter vs gunship battle, the team drops the EMP and assumedly defeat the Advisor(s). Dr. Magnusson entrusts them with one of two ansibles capable of controlling the satellite array; Dr. Kleiner gives Alyx her old family photograph. As they fly off for Adlivun Electric, Alyx is confident she can keep herself together after her father's loss. The chapter ends with Alyx beginning to question Barney's loyalty.

Dynamic Equilibrium: At Adlivun Electric, Gordon destroys the teleporter to keep Alyx out of the Combine's hands just before being captured himself. Dr. Mossman, using the lab's eqiupment in the hopes of destroying the Borealis, accidentally materializes Chell who reluctantly agrees to help them in exchange for freedom. Meanwhile, the battalion that captured Gordon tries to escort him to the Borealis but is massacred by a water creature. Chell finds him and sets him on his path to download Mossman's software at Siphon 3. Succeeding at this, the two are cornered by soldiers and flee through a mysterious tear to another world.