Its storyline centers on the circumstances surrounding a deceased scientist (Neal Huff), who was doped with a "designer virus" and transformed into a dangerous monster, causing his plane to crash.

Fringe agent Olivia Dunham (Anna Torv) and FBI consultants Peter (Joshua Jackson) and Walter Bishop (John Noble) connect the event to an impending arms deal.

Olivia must explore her mind for remaining memories of her former partner and lover, John Scott (Mark Valley), in order to prevent the sale of the virus.

Commentators have noted allusions to the pilot and a fourth-season episode, in addition to the television series Lost and H. G. Wells' novel The Island of Doctor Moreau.

On an airplane in flight, scientist Marshall Bowman (Neal Huff) gets a nosebleed, and he tries to warn the crew to give him sedatives or use force against him.

Back at the lab at Harvard, Walter finds a small crystalline disc implanted in the beast's hand similar to one seen inside the woman killed in "The Ghost Network", and thinks Marshall was dosed with a "designer virus".

After beginning to transform into a beast, he admits that "Conrad" dosed them before Peter Bishop (Joshua Jackson) pauses the process by administering a sedative and placing him in an induced coma.

French intelligence states that weapons manufacturer Conrad is involved in a sale, leading to Olivia returning to the sensory deprivation tank in order to find out more from Scott's memories.

The episode ends with Walter telling Olivia her brain waves are going back to normal, and that Scott's memories are fading from her mind.

Media outlets speculated that because Valley and Torv married over the holiday break, his departure "would eliminate any chances of the marriage conflicting with the show.

[4] Though the episode first aired in February 2009, "The Transformation" had an early screening at the November 2008 PaleyFest, where Fringe's producers answered questions from the audience.

[7] When asked in an interview if the "giant germ" from "Bound" was the grossest thing of the season, executive producer Jeff Pinkner replied that "the huge porcupine man on the airplane [from "The Transformation"] was more shocking.

The season's sixteenth episode, "Nothing As It Seems", centers around the "designer virus" that had caused Marshall Bowman to transform, but this time he does so in the airport after his plane has safely landed.

Andrew Hanson from the Los Angeles Times gave the episode a positive review, opining that it "hit the perfect tone for Fringe [and had] the right mixture of science fiction, dark comedy, crime story and melodrama".

He was pleased with the absence of Sanford Harris and enjoyed the "brilliantly written and directed" undercover sting operation, particularly because Peter was properly utilized as Olivia's "wingman.

If anything, it recapitulated pretty much every previous Fringe element—bio-weapons sales, telepathic communication, Massive Dynamics, [sic] airplane crashes, etc.—but did so in a way that was energetic, tense, and even a little emotional.

Though she thought it was "sweet" that Scott's proposal "echo[ed] the real-life recent marriage between Anna Torv and Mark Valley," Stegall was pleased that the series could now move onto another storyline.