Kendall is the one who reveals everything to Sydney. The episode begins with Sydney finding out from Kendall that the Covenant captured the Rambaldi cube while it was in transit. Sydney was captured by the Covenant after her fight with Allison, and was subjected to months of torture in an effort to brainwash her into thinking she was Julia Thorne. The brainwashing failed, but she pretended to be Thorne to remain alive and she contacted Kendall to let him know she was still alive. Kendall convinced her to continue the act in order to get info on the Covenant. She contacted Lazarey, who the Covenant wanted her to kill, and got him to help her find the cube with Rambaldi's DNA. Sydney helped Lazarey stage his death. They get the cube, but instead of giving it to Kendall, Sydney decides to hide it and then has her memory erased so that no one can ever find it. She begs Kendall not to reveal anything about what happened...not even telling her what happened after she lost her memory.
Sydney erased her own memory to prevent the cube from being found.
However, and this is where I'm a little hazy, Sloane gave her a key in an envelope addressed from Rome with her handwriting. She begins retracing her steps, eventually finding Lazarey, and the cube. Her plan to prevent the cube from getting out in the open failed, and Sloane looks highly suspicious right now. The DNA sample in the cube is supposed to bring about a "second coming". The Covenant operated on Sydney when she was captured and removed eggs from her ovaries, and plan on using the DNA sample in the cube to fertilize them. Thanks to Marshall, who planted a tracer on the cube, Sydney is able to find where the Covenant took the cube. Syd, Vaughn, Dixon, and Weiss stage a raid, destroy the lab, and rescue Lazarey. Sark is seen contacting someone to take care of Lazarey. As Lazarey is being taken to the hospital, he tries to tell Syd about "the passenger". However, as he is taken from the ambulence, he is killed by a sniper, who escapes.
The sniper turns out to be Lauren, Vaughn's wife.