The episode begins with Sheppard flying Zelenka and Ronon back from the mainland where Zelenka has been performing some scientific tests and Ronon was hunting – Ronon is in a foul mood cos the noise of Zelenka’s tests scared off any game! Sheppard suggests he try meditation lessons with Teyla. They suddenly realise that they should be able to see Atlantis but it’s not there. After a coupla moment of confusion Zelenka tells Sheppard to change course and they find the city right where it should be – the jumper’s navigational system is off. They get back to the city and Ronon joins Teyla for a meditation lesson… and falls asleep! Teyla is not too impressed when he starts snoring! Teyla leaves the meditation session and as she walks back to her quarters she sees an Ancient woman walking down the corridor towards her, speaking in a weird noises that Teyla cannot understand. Teyla tries to speak to her but the woman walks right through her and disappears.
Rodney bugs Elizabeth about his desire to keep all 3 ZPMs the city was left with after the replicator takeover. Elizabeth tells him it’s not possible – they need one for the Antarctica outpost and one for the Oddysey to help them in their fight against the Orii. Ronon and Teyla stick fight (and she kicks his ass!
) and as they walk through the corridors together afterwards, Teyla sees the Ancient woman again – Ronon can’t see her. This time, Teyla steps aside and lets the woman walk past her and follows as she walks up to a door which opens and a terribly burned man staggers out. The vision disappears leaving Teyla shocked and Ronon confused – he saw nothing.
Sheppard meets Rodney on a balcony where Rodney is using binoculars to watch the whale creature from GUP (he thinks it’s the same whale) swimming around not far from the city. Teyla has a brain scan which is clear with no sign of any abnormality. No-one can work out why she saw what she saw. Teyla theorises that perhaps she is seeing the “ghosts” of Ancients who died recently during the Asuran attack and who tried to ascend but were prevented from doing so fully and are trapped between planes of existence.
Rodney tells Weir and Sheppard that he has found information on the whale-like creature in the Ancient database. He mentions that “Sam” lead Sheppard and Zelenka to him in the submerged jumper and hastily covers up by saying he has named the whale Sam! Night time. Teyla gets into bed but before she can fall asleep she is disturbed by a noise – the same odd speech she heard the Ancient woman make before. She leaves her room and sees the same thing – the woman walks past her, the door opens and the burned man staggers out. This time before they disappear the woman catches the burned man and turns to, it seems, cry out for help. Teyla clutches her head as though the noise causes her pain.
Teyla talks to Heightmeyer about her visions and they discuss why they are appearing only to Teyla. Teyla thinks if the visions are Ancients trapped between planes, they may be trying to communicate and ask for help. Heightmeyer updates Weir on the situation with Teyla – after she leaves, Weir opens a transporter door to be confronted with the burned man. He disappears, leaving Weir shocked. Weir and Teyla discuss the visions with Heightmeyer and she thinks it may be the power of suggestion and that both Weir and Teyla are tired and need a break. Teyla has headaches and cannot sleep - Heightmeyer suggests both Weir and Teyla see Beckett for something to hekp them sleep.
McKay shows Sheppard that he has found a second whale on the scanners – possibly “Sam’s” mother. Sheppard claims calling the whale Sam is creepy but suggests they take a jumper and take a closer look at them. Zelenka warns them that he’s not yet sure he has fixed the problem with the navigational glitch but that he will track them from the control room. Beckett gives Weir and Teyla sleeping pills and tells them they should make time for at least 8 hours uninterrupted rest. After they leave, he sees a team of Ancient medics treating/operating on the burned man. They disappear.
McKay and Sheppard fly the jumper underwater to get a closer look at the whales. In a corridor on Atlantis, Ronon sees a team of Ancient scientists gathered around a console then they disappear. As they get closer to the whales, Sheppard starts to get a headache. They have a problem with navigation again and suddenly find themselves much closer to the whales than they intended to get. McKay gets a sudden headache too. They agree that it’s not a coincidence and decide to pull back. Zelenka suggests it may be the whales’ echo location system creating uncomfortable vibrations and causing the headaches. On the monitor Radek suddenly sees many more whales – dozens of them – heading for the jumper. McKay’s nose starts to bleed.
Weir, Beckett, Ronon and Teyla discuss with Heightmeyer that they have all seen the visions now and others in the city are starting to report seeing them. In all the visions the apparitions are Ancients and seem worried. Weir is called to the control room. Sheppard and McKay are trying to get away from the whales to alleviate the pain they are experiencing but the whales are cutting them off. Rodney passes out, bleeding from his ears. Sheppard decides they need to get out of the water now. His ears start bleeding too as he flies the jumper straight up out of the water. On the scanner, hundreds of whales are now heading to Atlantis.
In the infirmary, Sheppard and McKay are in bed and Beckett and Zelenka explain their eardrums have been perforated by the whales’ sonar. Close proximity to the whales’ communication is very dangerous to humans. Sheppard and McKay are partially deaf – though Beckett says it should heal soon – and are shouting when they talk!
Whales are approaching the city from every direction. Their communications are affecting the people in the city – people are experiencing headaches and nosebleeds etc and the closer the whales get, the worse it will get. They turn on the shield. Teyla suggests if the Ancient visions they are seeing are trying to warn them of something, perhaps this is it; her visions started when they first noticed the whale.
In the infirmary, Sheppard is starting to feel better – the pain is less and he thinks he hearing is getting better. He tries to tell McKay who doesn’t appear to hear him. Sheppard tests McKay’s deafness by making a few snide comments “Canadian football league’s a joke”, “Celine Dion is over-rated” and “Zelenka is smarter than you are!” No response from McKay who is working on a datapad – until he announces that he has found mention of a biolab the Ancients used to study animal life.
More people are getting ill – all Beckett can do is give people painkillers. McKay and Sheppard decide to leave the infirmary, saying they are feeling better. Beckett tries to order them back to bed but they explain about the Ancient biolab and that it might help solve their current situation.