Originally Posted by Zoopy_T

What was the plot? Why were there aliens?

In short: Wallace Breen, the BM administrator, is contacted by the Combine, a giant, multi-dimensional and pan-galactic empire, because they want to use him to conquer Earth (which he sees as bringing Earth into the folds of a far more advanced civilisation, which would stop wars, etc.; the usual sci-fi utopian scenario). They provide Breen with a crystal sample which, when exposed to the BM labs' mass spectrometer, will cause an explosive reaction that will tear a hole in the fabric of space and open several portals to the fringe dimension known as Xen.

The reason the Combine want an Earth-Xen portal to be open is this: a creature known as the Nihilanth, from a race of powerful telepathic creatures with the ability to mind-control other living beings, has taken refuge on Xen with an army it "stole" from the Combine. The Nihilanth's race, also know as the Controllers, were enslaved by the Combine several years prior to the BM incident, cybernetically augmented and used as enforcers in their armies. The Nihilanth somehow broke free of the Combine and ran to Xen with one of the Combine's armies, composed of various alien races (vortigaunts, bullsquids, headcrabs, houndeyes, etc. are all differents races enslaved by the Combine).

With the Earth-Xen portal open, the Nihilanth, already on the run, would move on to Earth, a planet rich in resources, weaponry and living beings that the Nihilanth can use against the Combine. Forcing the Nihilanth into doing that has three purposes: firstly, it allows the Combine to corner it on Earth, a place which is solidly grounded in reality, unlike Xen; secondly, it allows the Combine to actually reach Earth en masse using Xen as a routing point, whereas before, they were limited to expending great amounts of energy to send messages; thirdly, it prepares Earth for the arrival of the Combine by introducing its denizens to the very real existence of other-dimensional beings, HL1's "aliens."

This is where HL1 picks up. You're Gordon Freeman, on his first day of work at the BM complex. Your first task of the day is analysing a crystal sample of unknown origins using the labs' mass spectrometer. This causes the resonance cascade and the beginning of the portal storms. The Nihilant starts evacuating its forces to Earth for a final stand, in the face of an imminent Combine assault on Xen, which is why Xenians (as we'll call the Nihilanth's "coalition") keep appearing in BM.

Unfortunately for the Xenians, there's another player in the game: a god-like, immortal, quasi-ubiquitous independent mercenary contract broker whom we know as "the G-Man," who's working for the Combine (or possibly an unknown third party, or a seditious political faction within the Combine that don't agree with the enslavement of sentient races, or... your guess is as good as mine) against the Xenians. Early on, he spots Freeman and takes a liking to him; seeing promise in this new agent, he helps him here and there, and hinders him from time to time in order to shape him according to his desires.

The US military moves in to suppress the whole thing so no knowledge of aliens or irregular science experiments reaches the rest of the world. Freeman survives the initial chaos resulting from the incident, then the US Army assault, reaches some of his colleagues who've also been lucky, helps launch a satellite that will relay a particle beam from Earth to Dog-knows where, then is expedited to Xen using experimental teleport technology reverse-engineered from the Xen portals. You end up killing the Nihilanth, thereby terminating its control on the stolen legion and doing the Combine's work for them (though I'm sure they'd have preferred to recuperate their precious Controller king).

Upon your return to Earth, the G-Man actually introduces himself to you and expresses interest in you as an asset to be uses in his line of work. About to take flak for the way the whole Nihilanth thing was handled, he offers you the opportunity to work for him; you accept, and he whisks you away to somewhere out of the timestream.

Meanwhile, everywhere else on Earth, the first portal storms and the appearance of the Xenians have caused mass panic and chaos. The Combine move in shortly after, triggering the Seven Hour War, at the end of which Earth capitulates in negotiations lead by Dr. Wallace Breen. Ten years of Combine repression ensue, with them putting in place some sort of energy field to prevent humans from breeding, the portals forcing humans to hyper-urbanise and the world being governed by various human administrators working for the Combine.

That's more or less HL1's plot in a nutshell, or what I can remember of it.