Teyla's teammates fear that she's hallucinating when she claims to have encountered a ghostly Ancient woman and the specter of a badly burned Ancient man in the hallways of Atlantis. Soon, however, Weir glimpses the burned man, too. Beckett then spots an ethereal Ancient medical team working on the man in the infirmary. Even the pragmatic Ronon admits that he has witnessed ghostly scientists consulting one another. All the apparitions speak a strange, garbled language as they haunt the city's corridors.
Meanwhile, McKay discovers a pair of huge whale-like fish swimming near the city. When he and Sheppard fly a Puddle Jumper into the ocean to investigate, the creatures swim frighteningly close to them. Simultaneously, Sheppard and McKay are slammed with terrible headaches. Their ears start bleeding, and McKay passes out.
Sheppard barely flies the ship back to Atlantis. Intense, low-frequency pulses and electromagnetic fields emitted by the creatures have perforated his and McKay's eardrums. Worse, hundreds of the creatures are now swimming toward the city. As they draw near, more and more expedition members collapse under the crippling headaches caused by the creatures' proximity.
Certain that the creatures and the ghostly Ancients are connected, McKay and Sheppard drag themselves out of the infirmary and seek out a hitherto unexplored lab where the Ancients studied the planet's animal life. There, McKay discovers that the ghostly apparitions have been generated by the creatures, who receive and project information through acoustic and electromagnetic vibrations. The Ancients, knowing of the creatures' abilities, built a device to translate their communications - the garbled speech of the apparitions - into Ancient.
The creatures have a frantic warning to deliver. Approximately 15,000 years ago, this system's unstable sun convulsed with a coronal mass ejection, emitting an enormous burst of radiation. A courageous Ancient pilot - the burned man - warned the city of the danger before dying of radiation burns. Using their three Z.P.M.s, the Ancients then extended their shield to protect a huge section of the planet and its sentient aquatic creatures until the deadly radiation faded.
The whale-like creatures have sensed that another coronal mass ejection is imminent. The images they have been projecting as warnings were received by their ancestors 15,000 years ago, then passed down through genetic memory until now. This time, however, the city lacks the multiple Z.P.M.s needed to extend the shield. Atlantis's new inhabitants must find a totally different way to defend the planet - something even the Ancients never tried.