The end of season one of Lost left us looking into the interior of the hatch which had been blown open with the use of some explosives which had been found inside a wrecked ship on the island. It turns out that inside the hatch is a research station which has electricity and running water. It also has plenty of food stocked within it and an occupant called Desmond. According to Desmond the world will end if a sequence of numbers isn’t typed into the 1970’s era computer every 108 minutes. The problem is that the computer has been damaged during the attempt to access the station. It turns out though that Sayid also has some computer skills and fixes the computer just in time, but not before Desmond does a runner. The number sequence incidentally is 4, 8, 15, 16, 23, and 42
There is some debate as to whether or not Desmond is telling the truth about the consequences of not entering the numbers into the now fixed computer. However, the group decide to err on the side of caution and setup shifts so that the timetable can be kept.
The group do a bit of research inside the station and find some video instruction manuals which reveal that a group called the Dharma Initiative have set up a network of stations on the island. The one they are currently in is called the Swan Station.
While on a foray to try and find Vincent, Walt’s dog, Shannon comes across Walt but he is soaking wet and appears to be speaking backwards. Something else disconcerting about this encounter is that Walt appears to blink in and out of existence. Shannon thinks that something has happened to the guys that left of the raft and her fears worsen when she along with Claire come across the bottle of messages that was supposed to have been delivered by Sawyer, Walt, Jin and Michael to the mainland on the raft, washed up on the beach.
After the attack on the four survivors on the raft and the subsequent abduction of Walt and the disappearance of Jin, Michael and Sawyer construct another raft from the wreckage. The current carries them back to the island where they find Jin and another group of survivors. This group, led by Ana Lucia were in the tail section of the aircraft which crashed on a different part of the island. Other survivors introduced at this point are Mr. Eko and Libby.
After initially distrusting the newcomers and wanting to hold them captive, Ana Lucia agrees to travel to the other side of the island where the two main groups of survivors are now reunited.
Shannon and Sayid are starting to become something of an item and Shannon confides in Sayid, asking for his help, after revealing the visions of Walt she has been having. As Sayid and Shannon admit their love for each other Walt appears again, talking backwards. Shannon chases him into the jungle but startles an unprepared Ana Lucia who mistakes Shannon for one of The Others and shoots her dead. At this point we learn a little more about the experiences of the tail section survivors and the fact that 12 of their number have been abducted by The Others. Ana Lucia feels guilty about killing Shannon and although heartbroken at her loss, Sayid eventually comes to accept that it wasn’t her fault. This though leads to him developing a hatred of The Others.
Claire has to come to a decision about Charlie. He has been getting more and more paranoid about his need to protect Claire’s baby, so much so that he actually endangers his life at one point. Charlie eventually backs off and takes Mr Eko to see the Beechcraft and starts to grieve over the death of his brother who it turns out dies on that very plane. This inspires Mr Eko to believe in the power of the island so he begins to build a church on the island in order to repay his debt to Yemi.
Claire is forced to explore one of the other Dharma stations call the Staff in search of medicine when her baby falls ill. During her search she find out that one of The Others known as Tom wears a false beard. Why would they need to hide their identities?
A man identifying himself as Henry Gale from Minnesota apparently crashes on the island after being blown there in a balloon. He is captured by Rousseau and the group have doubts about his story, particularly Sayid, who still grieving for Shannon, tortures him while he is held captive in a small room inside The Swan.
During Locke’s shift at the computer he fails to enter the number in time and the station goes into lockdown mode. Only Henry Gale is able to get to the computer through the air vents and Locke instructs him to enter the code. As the countdown gets down to zero a blast door reveals the arrangement of stations on the island. Just as Locke starts to read the diagram, everything returns to normal in the station even though Gale says he never got to enter the code. It turns out though that Sayid was right and Gale isn’t who he says he is and admits to being one of The Others. This whole event though makes Locke doubt his faith in the island.
Eko and Locke discover a station called The Pearl station which seems to have been designed to monitor ongoings in all the other stations. Locke hypothesises that the whole thing about entering code numbers into the computer in The Swan station is a psychological experiment. Mr Eko though only redoubles his faith and is even more sure that entering the numbers is the right thing to do.
Meanwhile, Michael is on a mission to find his son, Walt. He uses The Swan’s computer to communicate with Walt and decides to go and find him but he is captured by The Others. When he is brought to what looks like The Others camp, a collection of huts, Michael is allowed three minutes to spend some time with Walt. Michael strikes a deal with The Others, but the price is quite high. Michael is released with instructions to go back to the camp and release Henry Gale. On top of this he has to persuade Jack, Kate, Sawyer and Hurley to go back to The Others camp at which point Walt will be released. Michael thinks that he will never get the group to agree to The Others’ terms and so sets about a plan of his own. He kills Ana Lucia and Libby and frees Henry Gale. He then shoots himself in the shoulder to make it look like Gale had escaped by himself. As the group hold a memorial for the two dead women, Desmond returns in a sailboat.
Michael puts together the next phase of his plan. Michael tells Jack, Kate, Sawyer and Hurley that he wants to raid The Others’ camp to rescue Walt and that he needs their help. Sayid isn’t convinced that Michael is being straight with them though and thinks that he is leading them into a trap. His plan consists of using Desmond’s sail boat to approach the camp from the seaward side. He gets Sun to translate for him and enlists the help of Jin as he knows how to sail. Although it has been revealed that Jin is infertile it has also been revealed that Sun is pregnant.
Even though Jack is aware of Michael’s plan, The Others are still successful in capturing him, Kate, Sawyer and Hurley. Henry Gale reveals himself to be the leader of The Others and keep his end of the bargain, allowing Michael and Walt to leave by boat. Hurley is told to go back to the survivors’ camp and tell them that they are never to return there.
Meanwhile, Sayid, Sun and Jin arrive at The Others camp and find it abandoned. They start a signal fire and sit and wait for Jack’s party to arrive.
Locke decides he wants to experiment with The Swan’s computer and the process of entering the numbers. He drafts in the help of Desmond and they both relieve Mr Eko. However, Desmond suddenly realises that the last time the code wasn’t entered in time was the day of the plane crash. The two argue over whether or not the threat is real but the counter reaches zero and a huge magnetic field is created. It seems this must have been the cause of the crash. Desmond reveals that there is a system termination station under the floor and leads the way to it. He activates the station by turning a key. The island is then engulfed in a bright white light and deluged with a loud shrill sound.