The mythology arc really kicks in with Ability. Written by David H. Goodman from a story by Glen Whitman and Robert Chiapetta this episode first aired on 10 February, 2009.
The story picks up with Mr. Jones (Jared Harris) escape from prison via the teleportation device, and its effect on him. It also reveals that he’s connected to a strange toxin that sealed all the orifices ln a person’s body. We get a glimpse of an Observer (Michael Cerveris) as it happens.
Harris will only deal with Olivia Dunham (Anna Torv), though Harris’ (Michael Gaston) oversight and audit of Fringe Division constantly gets in the way.
The toxin may be released on a city scale unless Olivia does what Jones wants, and it ties into an esoteric text that warns of a war against technology, hints against a conflict with another universe, and Harris’ belief that Olivia has been gifted with the abilities she needs to stop it all.
There are ties to Massive Dynamic and it brings a lot into question, especially about the nature of who Olivia is and what this strange ability, if it is such a thing, really is.
And while Peter (Joshua Jackson), Walter (John Noble), and Astrid (Jasika Nicole) pop up in the story, this is very much an Olivia-centric tale plunging us deeper into what is going on, and leaving us wondering what the hell the teleportation device does to a person after they use it.
William Bell, the owner of Massive Dynamic gets name-checked again and an unusual drug gets tied to Olivia’s past, and the text that Jones raves about may have been written by Walter, or at least on his typewriter.

Inner Child was written by Brad Kane and Julia Cho. It first debuted on 7 April, 2009.
Mystery arrives in the form of a strange young child (Spencer List) who has been sealed in a room for more than half a century. Mixed in with that is the reappearance of someone known as The Artist (Jeremy Shamos), whom Olivia and Charlie (Kirk Acevedo) have been trying to track down.
The Artist is a serial killer, he’s eluded capture for a long time, but this child may be able to help Olivia and the team to capture him, and put him behind bars once and for all.
No one, not even Walter, knows exactly the true nature of the child, or how he could have survived for so long. But he looks like a child version of the Observer, perhaps why they take such an interest in one another when one appears.
The child is interesting and makes a connection with Olivia, but he feels almost like a plot device to move the serial killer story along
And knowing part of what’s to come, it’s interesting to see all the seeds that are being planted around Peter.
It’s a fun ride.