Actors Anna Torv, John Noble, and Joshua Jackson reprised their roles as FBI agent Olivia Dunham and father-son duo Walter and Peter Bishop, respectively.

It was set in the former, until the last several episodes when Peter Bishop (Jackson) journeyed back to the parallel universe after being lured there by his real father, "Walternate" (Noble).

Massive Dynamic's Nina Sharp directs her to Sam Weiss, a bowling alley manager, who gives her cryptic but helpful advice to overcome her amnesia.

Meanwhile, the Fringe division has discovered several shapeshifters - a human/machine hybrid that bleed mercury - have crossed over, but unbeknownst to them, one takes the form of Olivia's partner, Charlie.

Initially unable to do so, her fear of failure enables her ability, allowing them to save the people within the target building, but also revealing to her that Peter is from the parallel universe.

Walter explains to Olivia that in 1985, he and Bell had devised a way to observe the parallel universe, where he found his doppelgänger, "Walternate", was also close to losing his son.

Though Walter's Peter had died, Walternate continued to search for a cure, but missed the telltale sign when the Observer September arrived at his lab.

Walter resynthesized the cure and aimed to cross over using untested equipment at Reiden Lake, though stalled by Nina and his lab assistant Clara.

Olivia and Walter are alerted by September that Walternate plans to use Peter to initiate the operation of a strange device that threatens to destroy the prime universe, and the two launch a rescue attempt.

In the parallel universe, they find that it suffers from singularities caused by Walter's crossing in 1985, forcing Walternate's Fringe team to use an amber-like substance to surround and quarantine such areas, regardless of innocent lives trapped within.

Olivia faces off against her doppelgänger, "Fauxlivia", who works for Walternate in the Fringe Division under the U.S. Secretary of Defense; she is able to recover Peter, who has seen the device and recognized that it reacted only to his biology, and wants nothing of it, willing to return with the others.

[27][28] Fringe consequently got a mostly new writing staff and production team, though co-creators J. J. Abrams, Roberto Orci, and Alex Kurtzman, and producer Bryan Burk remained involved with the series.

"[40] They wanted to make the three main cast members become more comfortable as a team in Fringe Division; Peter thus was written to be more heroic and to go from reluctance to a desire to help his father, while Walter became gradually more independent and "grounded as a human being".

[33] Throughout the season, Pinkner and Wyman tried to create an episode that best bridged "standalone" traits—needed for casual viewers—with the further advancement of the show's mythology for those who watched regularly.

"[41] The Fringe producers strove to avoid becoming bogged down in mythology, an issue that they perceived happened in Alias, another J. J. Abrams television series.

In a joint statement released midway through the season, Abrams, Pinkner, and Wyman noted that their "only internal rule is that we make every effort to not raise mythological questions merely to string viewers along, but rather to provide answers that generate consequences.

[43][44][45] While the episode already had most of the necessary elements in place before Fox's request, the producers were able to add the musical theme as a "narrative device" to "explore Walter's feelings" in the aftermath of Peter's discovery and flight.

One time guest directors for the season included Bryan Spicer,[50] Jon Cassar,[51] Dennis Smith,[52] Paul Holahan,[53] Jeannot Szwarc,[54] Frederick E. O. Toye,[note 1] Deran Sarafian,[56] Adam Davidson,[57] Charles Beeson,[58] David Straiton,[59] Thomas Yatsko,[60] Jeffrey Hunt,[61] and Seith Mann.

Anna Torv played determined FBI agent Olivia Dunham, who is able to travel between universes as a result of childhood experiments performed on her with the nootropic drug, Cortexiphan.

[71] Ryan McDonald portrayed Massive Dynamic scientist Brandon Fayette,[72][73] while its founder, Dr. William Bell was played by Leonard Nimoy, despite the actor's recent retirement.

Karen Holness appeared as Broyles' ex-wife Diane,[85] and Clark Middleton played rare book seller Edward Markham.

[86] Philip Winchester appeared as Fauxlivia's boyfriend Frank Stanton,[87][88] while Seth Gabel played Agent Lincoln Lee from the parallel universe, both in the finale.

[51] Further notable guest stars included Andrew Airlie,[90] Stefan Arngrim,[91][92] Demore Barnes,[56] Jenni Blong,[59] Pascale Hutton, Ravil Isyanov,[51] Ravi Kapoor,[93] Alice Kremelberg,[55] Diane Kruger,[94] Quinn Lord,[59] Tzi Ma,[53] Stephen McHattie,[50] Jennifer Missoni,[52] Cameron Monaghan,[90] Michael O'Neill,[95] Geoff Pierson,[56] Martha Plimpton,[96] Paul Rae,[52] John Savage,[92] Peter Weller,[97] and Craig Robert Young.

[106] However, Fringe and its lead-in, Bones, did help the network increase 52% among adults aged 18–49 and 65 percent among total viewers from the same night the previous year.

At the beginning of the season, the series was featured on the September 18 cover of Entertainment Weekly, which promised to give readers a "deep dive into the gory, witty world of Fox's Fringe".

The website's critical consensus reads, "Fringe surpasses expectations in season two with stronger character development while maintaining its creepy sci-fi angle.

[111] After viewing the first eight episodes, Entertainment Weekly columnist Ken Tucker gave the series an A−, calling it "one of the fastest, smartest, wittiest shows on television now...

He believed the second season had "floundered a little, stuck in that creative hinterland between the desire to grab new viewers and the need to build on the mythology of the show's universe.

Club agreed, and called the first half "entertaining" but "never essential" while noting a great improvement mid-way through the season, as "the show finally grounded its freak-of-the-week weirdness in deep sadness".

Special features on the sets include four commentary tracks—"Momentum Deferred" with Jill Risk, Matthew Pitts, Danielle Dispaltro, Justin Doble and Charles Scott IV; "Peter" with John Noble, Blair Brown and Damian Holbrook; "Brown Betty" with Tanya Swerling, Billy Gottlieb, Chris Tilton and Jay Worth; and "Over There, Part 2" with Jeff Pinkner, J. H. Wyman and Akiva Goldsman.