The Xenian crystal is a peice of grist that the G-man (a First Guardian) acquired for the government and his own purposes. The result is an interdemensional rift linking Earth with a Vortigaunt session.
On top of the Reckoning, they're dealing with an Alternian invasion of their homeworld. A significant portion of the fleet gets pulled into the session along with the Vortigaunts who's social structure and culture causes for large scale sessions with wide areas transported into the Medium with them.
The Combine Advisors are various Mother Grubs who are going to have to compete for the right to mother a new Alternia, but in the mean time they need to de-terraform Earth to their liking.
This also explains the Synth, a bio-mechanical race dedicated to their overlords.
Charlie Tunoku is a lover and a fighter.