It was the third Fringe episode to be written by supervising producer Jeff Vlaming, while it was director Deran Sarafian's only credit for the series to date.

The building is quarantined with Walter's son Peter (Joshua Jackson), FBI agent Olivia (Anna Torv), and the rest of the witnesses still inside.

As a bio-hazard team enters the building to test people for the virus, a CDC official orders the army to prepare for a "level six eradication", because they still do not know how to contain it.

Walter realizes that sulfuric ash killed the virus thousands of years ago, and successfully finds a cure with some horseradish he found in the office break room.

The CDC agrees to allow Olivia to enter the building and use the air ventilation system to spread some fentanyl gas, which will gain them time while the cure is synthesized.

[6] The episode featured one-time guest appearances by actors Demore Barnes, Geoff Pierson, Conrad Coates, Natassia Malthe, and David Richmond-Peck.

[7] Actor Joshua Jackson, who plays an infected Peter Bishop in the episode, noted during shooting that he found inspiration from "imagin[ing] the worst hangover I've ever had and multiply it by ten".

"[10] IGN's Ramsey Isler also found the episode average and predictable, as it lacked "much of the quintessential storytelling elements that, once upon a time, made this one of the best shows on TV.

[2] TV Squad columnist Jane Boursaw thought Walter discovering a cure was a little far-fetched, and wished Broyles was a greater part of the show.

[12] Andrew Hanson from the Los Angeles Times thought it was a really good episode, and even wished it could have been turned into a movie, were Fringe to get into filmmaking.

[13] Josh Wigler of MTV thought it was a "pretty cool" mystery-of-the-week, and "while not quite as strong as when the mythology is in full gear, 'What Lies Below' was nonetheless a compelling hour of television."

"[14] Director Deran Sarafian submitted "What Lies Below" for consideration in the Outstanding Directing for a Drama Series category at the 62nd Primetime Emmy Awards.