Gordon Freeman and Chell start an adventure together in the battle for finding Borealis.The game has 4 big parts:
1.Gordon Freeman(Darker Mesa) where he starts from embarking the transit train and ride to its sector,then fight other Zen and headcrabs,and newer enemies.After that,G-Man will apear and will tell him that is going to meet a special person later on(Chell).Then he finds himself with Alyx and Dog at a helicopter bay,where they embark to fly to their destination:Arctic.
2.Chell(Aperture Technologies)where Chell is back in Aperture Science with GlaDOS.She tells Chell that somebody wearing a tie just teleported in her chamber.Then Chell goes to sleep in a cyro chamber,then she wakes up in Aperture City for Test Subjects and Test Robots.She meets first G-Man in dark alley and then makes her daily testing to be healty.G-Man tells her she haves two choices:Meet Freeman(wich she never heard of before,only in her vision when seeing G-Man)or to stay in Aperture Technologies wich will be blown by Combine helicopters.She can either choose to go or stay.If she chooses to go,she will team up with other test subjects and finally meet with Doug Rattman.He is scared at first to go in GlaDOS'chamber so he will follow them through some test chambers,hidden by the cameras.Finally he gets some courage after eating beans and taking pills.Then the gang goes at GlaDOS'chamber where GlaDOS almost kills Rattman for living in the facility for so long.Then she gives some devices to the portal guns from Chell and the other 2 test subjects.They all leave finally Aperture Science(through the gate from the ending in portal 1) and take a Aperture Science Car and leave to go to Arctic.
3.Foreseen consequences where Chell and Freeman finally meet.Then Alyx is surprised to see her there.She tells Chell she teleported by accident to a weird place called Aperture Science and has seen her completing a test chamber.Then(Chell and Freeman)show their ablities from their guns.After starting to head to the boat that will lead them to Borealis,they meet G-Man walking in the snow during a snow storm accompanied by four Xen(as his bodyguards,they don't attack them) and tells them about their service is about to end and walks further back to the helicopter and flies away.Then,at the boat they meet Barney,Calhoun(from HL Blue Shift) and the character from Opposing force,along with Doctor Mickleschutz(met by Freeman in part 1 in Black Mesa) and embark the boat.
4.Borealis where G-Man appears and says'You shouldn't be here....As my "sources" tell me that you have found Borealis,but your services have ended,so i don't want you around to mess with my "sources" and other hired humans.'(and then they get teleported to an iceberg sinking,from where they escape through a portal made by Chell.They get weapons from a storage shed and they discover a fusion device.They use the Portal Gun and the Gravity Gun in the device and they fusion to a new device,the 'Gravonator' gun.Then Freeman takes the guns and leaves Chell to handle the Gravonator.They test the weapons and train themselves so they can get back on Borealis.Speaking of Borealis,they see the ship starting to move through the frozen sea.They jump on the ship and start a epic fight.They have a limited time(30 minutes)to defeat all enemies and take control of the ship or they will sink with Borealis after falling on a Waterfall.They gain the control of their ship and they turn it around.G-Man is again teleporting in the cabin of the ship and tells them:'I may have been mistaken your abilities,Freeman and Chell,and oh,them(refers to Barney,Alyx,Dog and the Opposing Force character) and you have all passed a test so you can be again under my service'
Then they return the Borealis to Aperture Science,GlaDOS organizes a trip to Arctic for scientists so Aperture science and Black Mesa will stop their rivalry and wil become a new company:Aperture Mesa.
This can be found in the hiring document too for entering the team