Thanks to IO9 We have an official description of Enemy at the gate, the final episode of Stargate Atlantis Season 5:
Todd contacts Atlantis and reveals that a Wraith subordinate has managed to acquire several Zero Point Modules that he has used to power a formidable new hive ship. He urges Woolsey to attack and destroy before it becomes a threat to Atlantis.
On board the Daedalus, Colonel Caldwell, Colonel Sheppard and the rest of the team, rush to engage the new hive ship. But the Z.P.M. powered vessel proves itself an impressive opponent, crippling the Daedalus before making a sudden and inexplicable jump into hyperspace.
Puzzled over the Wraith’s sudden departure, the team picks up a weak subspace signal in Wraith code. McKay is quick to recognize that the communique was sent, through subspace, from another reality. Once deciphered, their worst fears are realized. The Wraith message contains a familiar set of coordinates. The hive ship is on its way to Earth!
And here what was said about this final Stargate Atlantis episode in the past:
I really hope it doesn’t end on a cliffhanger: I’d be pissed off if I had to wait the future Stargate Atlantis movie…