Everything started at the Black Mesa Research Faciility located in United States of America in the state of New Mexico. During this time Dr. Wallace Breen was the administrator of the research facility and is mostly believed to be responsible for the events on May 16th, 200X. Depending on your perspective you may blame others for the current state of Earth, including Dr. Vance, Dr. Kleiner and even Gordon Freeman himself. To some it doesn't matter who caused this series of unfortunate events as long as everyone is doing their part to reclaim humanity's freedom. Regardless of whose fault it was, that was the day shit hit the fan. As soon as Xen crystal sample "GG-3883" was pushed into the Anti-Mass Spectrometer, it caused a Resonance Cascade powerful enought to open an inter-dimensional rift. Even though later on the rift was close, this didn't stop Portal Storms opening across Earth from which the combine arrived.
That is the simplier version of events but how did pushing some orange crystal into a laser cause all this? Well, every object has a set resonance (hence the named Resonance Cascade). The object will resonate if hit with specific forms of energy at the correct frequency. If crystals like the ones found on Xen resonate too much it can open portals and tear dimensional rifts like the ones seen on May 16th.
As of right now, the best we can do to defend against another Resonance Cascade or other form of portal is to just prevent them in the first place. We're currently working on a solution that doesn't involve a NASA rocket because those are pretty difficult to come by.