Official Entry: "The Alien scare first began on 7th March, 2084 when a strange Dimension Gate appeared in the skies above Mega-Primus. During the following days strange UFOs came and went, but they did not appear to attack anything or abduct anyone. It was only when strange reports of Alien monsters lurking in the recesses of city buildings filtered through to the senatorial security committee that the plan to enlist X-COM was proposed."
They will use a number of means to obtain their goals: infiltration, subversion and outright aggression against any organization(s) that stands in their path. It will be up to X-COM to discover the nature of this new alien threat and to defeat it.
In terms of relations, the Aliens are treated as an Organization. This means that other organizations may come to consider them friends. In that case, X-COM's relations with those organizations will suffer each time X-COM destroys Alien forces; conversely, X-COM's relations with organizations that are on bad terms with the Aliens will improve.