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Half Life 1 didn't make any sense because of horrible graphics and time put into it.
When HL1 was released it has the best graphics. Actually it does make perfect sense. Your Gordon Freeman a scientist at Black Mesa. Black Mesa use to be an old nuclear missile site. The day that you play involves testing this new crystal recently found. There seemed to be some conflict between the Scientist and Employers about actually testing it. Anyways while testing the crystal, basically something goes horribly wrong.
Xen. What is it? Xen is a border world between this universe and the next. Xen in HL2 and Blue Shift is used as a sling shot for teleportation. Well when happened when you pushed that crystal in is you basically opened up a portal and collided your world and Xen's. They then figure out that they can possible use this for teleportation in Blue Shift, right at the end.
In HL1 the vortigaunts had these gold cuffs around there hands. This is because Xen was invaded before. The HL1 Boss infact had these cuffs, was cut up.
The military and the coverup. They don't want to let this get out. The army is sent in to invade and kill everyone, leaving no survivors. Well then secret assassins are sent in to kill them for a final coverup. The Assassins are much more trusted than...loud mouth marines...
After Opposing Force you see the Black Mesa facility nuked.
Well this collision between you and Xen caught the eye of some other power... The Combine. The combine attacked earth, not with the "combine soliders" or anything but with there real power. They didn't have the soliders because the soliders are humans. The Combine basically a race that is made up of tons of races. What they did was smart, they took humans, screwed up their mind, used them as soliders. We have yet to see there real firepower besides Striders.
They launched citadels into major cities as a first strike. They used Xen creatures and Antlions to push people into the major cities where they could easily contain them. The war between the Combine lasted 7 hours then Breen negotiated earths Surrender and was givin power for it.
Breen is not a bad guy. He wants to preserve the human race by giving into the Combine. The Resistance wants to preserve the human race by standing up and fighting. As Gabe Newell said, one is wrong, the other is extremely wrong.
After about 10/15 years of combine control this is where you come when HL2 starts.
On another note the Combine have no way of teleporting short distances. The Combine can only teleport from lets say planet to planet. This is why in HL2 they were spying on Black Mesa East Labs. To get this technology of teleporting short distances. What Breen was hoping to show is that humans are useful.