In the Pilot Ep, Olivia mentions that she had prosecuted Broyle's best friend who had sexually assaulted some young Marine Privates and had him Jailed for it. Here we get to meet that scumbag in the form of Sanford Harris.
By now, we should have known that not one idle word is ever spoken in any Fringe episode, that won't be fleshed out in full later.
Before the Christmas Break, Olivia had been kidnapped by agents of David Robert Jones. This episode continues with that abduction - Which Walter and Peter do not know has happened yet.
It is apparently the next morning after the Little Hill Field incident, the last anyone had seen of Olivia was that she was on her way to Little Hill Field to try to stop what had gone on in S1E10. Peter arrives at the lab just as Walter is giving LSD to a hapless caterpillar, which changes colours in protest to Walter's chemical intrusion. For the first time in Fringe, Peter is not weirded out by Walter doing this.
We had learned a lot of things before the break, such as Peter had been Ill as a child and Walter had made a special Machine which could possibly transport people in space and time. We are about to learn a whole lot of new things.
As Olivia is bound in a makeshift laboratory, she is tilted upside-down and she sees a remarkable pair of shoes: File for Future reference. Her abductors then take Spinal Fluid.
But she escapes and steals one of the Black SUVs that were used in her abduction, and as she leaves the Lab, she grabs a bunch of Vials of some unknown substance, which she buries.
She calls this in and Broyles begins a full fledged operation: at that moment he gets a call from his "buddy" Sanford Harris: The very same pest that Olivia had put in Jail for sexual assault: who suddenly is not only free from Jail, but in now a high ranker in the Department of Homeland Security and mysteriously also in Charge of Auditing Fringe Division.
Thus begins a pain in Fringe Division's Side that continues until the season finale of this incredible first season of Fringe. Harris instantly cancels Broyles investigation of Olivia's Abduction and to top it off, she is collected by some guys in Black-The next we see, she is in a Hospital, handcuffed to a bed while Harris gloats about the "power he has been given."
Enter Rachel, Olivia's Sister and her daughter Ella, Olivia's Niece, who meet Olivia in the Hospital. After Olivia deals with the Red Tape Harris has set up in the FBI office, she contacts Walter and Peter and they meet her at the place where she hid the Vials of Unknown Gunk, which Walter identifies right away using a mobile laboratory.
This episode then segues into a MOTW - A Man is giving a lecture to a room full of Students, and he starts choking — after which a huge slimy worm-thing forces it's way out of his mouth, and scurries out into the crowd of Students, scaring their pants off.
Fringe Division is called in right away and Walter catches the thing under a trash can with the comment "Stuff like this used to happen all the time."
In his Lab, Walter identifies the thing as a huge Common Cold Virus.
This all turns out to be activity by ZFT, the stuff Olivia had hidden was used to create the huge version of Cold Virus. Olivia figures out that the Teacher, and another man, are epidemiologists who had been invited to join the CDC and nobody had known about that. Olivia tries to bring in the second scientist for protection but he is dosed with the Mega-Virus and this gives Walter one he can Dissect.
IN the middle of all of this, Olivia sees the remarkable Loafers that her abductor was wearing: On Mitchell Loeb's Feet! With Loeb identified as her Abductor she goes to his house to find clues, but is forced to face off with Samantha Loeb, again played by Trini Alvarado who she has to kill in Self-Defense. But now she has Proof that Loeb is a double-agent for ZFT and manages to drag a confession out of him despite interference from Harris.
Loeb, shocked by the death of his wife at Olivia's hands - Breaks down - And asks Olivia, "Do you not understand what we're up against? We saved you, we saved you!" - But what Mitchell will not tell Olivia, is WHY.
The seriousness with which Loeb says this gives Olivia Pause - Peter just assumes Loeb was trying to get back at Olivia, but it seems that Olivia has never bought this explanation.
Why is Jones so Interested in Olivia? If Loeb was not just trying to get back at Olivia, then the question becomes: Why? Why Olivia? Why take a Spinal Tap? Why Kidnap her? Why turn huge rabbit-sized Viruses loose? Why Kill People?
The Loeb character is revealed as a tragic character: in his mind he was not doing wrong, and if he was protecting Olivia then why tell his wife to Kill her?
The shadows of right and wrong are clearly mixed up from this point on - And things are not as simple as they once seemed in the Blue Universe. From this point on, the story being told starts becoming so much larger than anyone had ever imagined.
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