@tennmuerti: The story is that you lost at the very beginning of XCOM:EU and that your play-through EU was you playing the virtual tactics simulation run by the aliens inside your head using the chip. So technical XCOM:EU didn't happen and this is your first "real" campaign against the Aliens. That sounds like reboot logic to me. This is explained in the first hour of the game, there never was a XCOM vs Alien's they just swept in and wrecked us on the first mission. Then captured the commander and ran simulations in his brain. (The flash backs to XCOM:EU gameplay represent your whole EU campaign.
To be fair the way the premise is setup and explained is terrible, and fits the reboot theme of "Don't worry about part 1! It didn't happen!"