All descriptions but the ones with a link to them at the top belong to Quest Enterprises.
The Darkest Fathoms and Escape to Questworld descriptions were written by me, and the rest will be done in a similar style as soon as I have the time.
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01. THE DARKEST FATHOMS
First aired: 08/26/96
Main Characters Present: Jonny, Jessie, Hadji, Race, Dr. Quest
Episode Rating: 4/10
Quote: "O'er the waves of blood sail the Ivory Web - Filling all hearts with fear and dread - Though time has passed since I ravaged these seas - No one shall have what was Black Jack Lee's"
Summary: While a small ship was searching for oil off the coast of Bermuda, they found a ship - "The Ivory Web". When finding this ship, some "ghost pirates" attacked their ship.
The captain of the expedition, Lacey, afterwards goes to Dr. Quest asking for help since he lost 2 men and believes it was Lee's ghost. After looking a little farther into the history of Lee, he was intrigued and decides that he and the Quest Team should investigate the scene.
While Hadji, Jonny, and Race are underwater looking at the ship, "Lee's crew" overtakes the Quest's above the water, taking Jessie and Dr. Quest with them.
While on their way back to the ship, Race is injured. Leaving Jonny to go looking for Jessie and his dad, while Hadji stays back and tends to the ship and Race.
Credits:
Writers: Peter Lawrence and Harve Zimmel
Story Polish: Michael Ryan
Producer: John Eng
Guest Voices:
Charlie - Michael Benyaer
Black Jack Lee - Jeffrey Tambor
Gun Captain/Diver #1 - Jeff Bennett
Lacey/Pirate - Jim Cummings
Diver #2/Technician -- Paul Mercier
Black Jack Lee Imposter/Pirate #1 - Jim Meskimen
Pirate #2/#3 - Nick Tate
Commander - Paxton Whitehead
Mistakes: Submit One
Galleries:
Online Pictures
ScreenCaps

02. ESCAPE TO QUESTWORLD
First aired: 08/27/96
Main Characters Present: Jonny, Jessie, Hadji, Race, Dr. Quest
Episode Rating: 7/10
Quote: "Oh, Jonny Quest, do you really understand the entity you've unleashed upon your world!?"
Other Notes: First appearance of Jeremiah Surd, Julia, and Lorenzo.
First use of Questworld.
Summary: In 1978, Surd hid nerve gas in a building in Chicago because he lost government funding. 20 (+/-) years later, the gas was found during construction, leaving 2 workers dead.
The government asks Race to help them stop it from being released into the city because he was there the day that Surd was claimed as dead when originally trying to release it into the city. After agreeing, he and Dr. Quest search the building for the right cords to cut.
After finding out that Surd is still alive, Jonny, Jessie and Hadji go to the hospital he is being held in to try to ask him how to save their fathers. In exchange for his help, they gave him access to Questworld. He agrees to help, but with a 20-year grudge on Race Bannon, can they trust him?
Credits:
Writers: Richard Merwin and Peter Lawrence
Questworld Sequences by Michael Ryan
Producer: John Eng
Guest Voices:
Swat Member -- J.D. Roth
Surd/Guard/Quest Computer/Cop -- Frank Welker
Julie -- Megan Cavanagh
Lorenzo -- Chick Vennera
Bennett -- Paul Eiding
Mistakes: Submit One
Galleries:
Online Pictures
ScreenCaps
03. IN THE REALM OF THE CONDOR
First aired: 08/28/96
Notes: Despite the similarites of name and appearance, Estella Scheele is not an early version of Estella Velazquez, Jessie's mother ("Mummies of Malenque").
Summary: The Quest team follows Estella Scheele to find her missing ornithologist grandfather, and ends up finding the lost golden city of El Dorado.
04. RAGE'S BURNING WHEEL
First aired: 08/29/96
Notes: First appearance of Ezekiel Rage - though it's obvious that his first appeance should have been in "Ezekiel Rage" (#09). Due to production problems or continuity error . . . we'll never know.
Summary: Apocalyptist Ezekiel Rage hijacks the space shuttle carrying Dr Quest and Hadji. Back on Earth, Jonny and Jessie must find a way to stop Rage's apostles who have taken over Mission Control.
05. NDOVU'S LAST JOURNEY
First aired: 08/30/96
Summary: Jonny, Jessie and Hadji track an elephant, Ndovu, as it returns to the elephants' graveyard. On the way, they run into poachers who aren't willing to wait for Ndovu to die.
06. MANHATTAN MANEATER
First aired: 09/02/96
Summary: When a tiger gets loose in New York, Jonny and his friends track it to the disused subway tunnels underground - and so does a sleazy tabloid TV host.
07. EAST OF ZANZIBAR
First aired: 09/03/96
Notes: First appearance of Capt. Havell.
Summary: Are sea monsters responsible for the disappearance of ships in the Seychelles? The Quest team heads to the Indian Ocean to find out.
08. ASSAULT ON QUESTWORLD
First aired: 09/04/96
Summary: With Benton Quest and Race Bannon attending a phenomenology conference in the Himalayas, Jonny and Jessie are forced to impersonate their fathers in Questworld when Jeremiah Surd launches a two-pronged attack on the Quest compound - and Hadji's mind.
09. EZEKIEL RAGE
First aired: 09/05/96
Summary: Ezekiel Rage, a government agent who lost his family in a covert operation gone wrong, swears vengeance. Unfortunately for the Quest team who are out looking for a naturalist, they get in Rage's way.
10. ALIEN IN WASHINGTON
First aired: 09/06/96
Summary: Extraterrestrial transmissions turn out to be warnings to stop a series of space experiments, and the Vice President turns out to be an alien in this showcase for computer 3-D animation.
11. RETURN OF THE ANASAZI
First aired: 09/09/96
Notes: First appearance of Alice Starseer.
Summary: Alice Starseer, an old friend of Dr Quest, sends him a strange quartz statue that sends him, Race and Hadji to New Mexico. Back home, Jonny and Jessie discover that there's more to the statue than meets the eye - and that Men in Black are after it.
12. THE ALCHEMIST
First aired: 09/10/96
Summary: Dr Quest is commissioned to find the Philosopher's Stone, which is reputed to turn dross to gold. But when he succeeds, the stone is later stolen from a museum by Quest's partner, who wants to try it out for himself.
13. TROUBLE ON THE COLORADO
First aired: 09/11/96
Summary: Alice Starseer returns to Earth to lay her grandfather to rest. But Jeremiah Surd is determined to find out what she's learned.
14. IN THE WAKE OF MARY CELESTE
First aired: 09/12/96
Summary: A century ago, the cargo ship Mary Celeste sank under mysterious circumstances. While on an expedition to find the Mary Celeste's remains, Dr Quest discovers what look like crop circles at the bottom of the Sargasso Sea - and a graveyard of ships in an area barren of marine life.
15. AMOK
First aired: 09/13/96
Summary: On an archaeological expedition in Borneo, the Quest team run into a giant creature, reputed to savagely attack from all directions at the same time. Then they find out that man can be the greater beast...
16. BESIEGED IN PARADISE
First aired: 09/14/96
Summary: Jeremiah Surd taps into, and gains control of, the cetacean communications bandwidth, prodding cetaceans worldwide into savage attacks. The Quest team enlists the help of Captain Havell to stop Surd.
17. THE SPECTRE OF THE PINE BARRENS
First aired: 09/17/96
Summary: Dr Quest, Jonny and Hadji head to New Jersey to investigate the Jersey Devil. Then they run into a two-hundred-year-old feud between descendants of the Redcoats and the Minutemen over the original copy of the Declaration of Independence.
18. MUMMIES OF MALENQUE
First aired: 09/18/96
Notes: First appearance of Estella Velasquez.
Summary: During an expedition with Jessie's mother Estella, the Quest team discovers a plague that wiped out an ancient Inca-like tribe.
19. THE BALLAD OF BELLE BONNET
First aired: 09/19/96
Summary: Centuries ago, a female thief stole a wagonload of gold to help an Indian school stay open, but the gold - and the thief - were lost in vast caverns under the American desert. Jonny discovers that her ghost is still guarding the cache.
20. IN THE DARKNESS OF THE MOON
First aired: 09/23/96
Summary: A werewolf attack in northern Canada brings the Quest team to investigate. Race finds romance with an attractive outback doctor who turns out to be the last female descendant of a werewolf family.
21. THE SECRET OF THE MOAI
First aired: 09/24/96
Summary: An alien craft discovered on Easter Island seems to contain the missing link. But when Dr Quest and Race enter Questworld to investigate what they've found, they run into Jeremiah Surd - who wants to experiment with human de-evolution.
22. EXPEDITION TO KHUMBU
First aired: 09/25/96
Summary: Dr Quest goes missing on an expedition to find the Yeti. Jonny and his friends head to the Himalayas to find him, but run into another scientist who's determined to bring back the Yeti -- dead or alive.
23. ICE WILL BURN
First aired: 09/26/96
Summary: Jessie's plane goes down as she heads to join the Quest team in Northern Siberia. She discovers a colony of ancient Russians living underground.
24. ROCK OF RAGES
First aired: 09/28/96
Notes: First appearance of Pres. Elena Stasny and first appearance of General Vostok.
Summary: The Quest team journeys to the Czech Republic to help translate an artifact that's supposed to be the key to controlling a Golem. They run afoul of an ex-KGB operative who's determined to reactivate the Golem to overthrow the government.
25. HEROES
First aired: 09/18/96
Summary: When Dr Quest uses Questworld to help reassemble a shattered Apollo statue, Jeremiah Surd steals the show and lures Jonny into a labyrinth of horrors.
26. FUTURE RAGE
First aired: 10/29/96
Summary: Ezekiel Rage steals a compact nuclear device and plans to blow up the polar ice caps. The Aurora Borealis hold the key to stopping him.
27. ALLIGATORS AND OKEECHOBEE VIKINGS
First aired: 11/01/96
Summary: "Alligators" attack a drilling facility in the Florida Everglades, and leave behind an ornate Viking sword. But when the Quest team heads out to investigate, they find a different set of villains at work.
28. BLOODLINES
First aired: 12/13/96
Notes: First appearance of Pasha (in this series) and Hadji's biological family.
Summary: Hadji discovers the truth about his past when a troubling memory of Pasha sends him to Calcutta in search of his former guardian.
29. RACE AGAINST DANGER
First aired: 12/16/96
Summary: Race has to cross an obstacle course where he set the record for Special Forces recruits -- but there've been some modifications since he was last there.
30. THE DARK MOUNTAIN
First aired: 12/17/96
Summary: Is Bigfoot on the loose in the Quest compound? More importantly, why is he stealing electronic components? The Quest team has to find the answers before a couple of big-game hunters bag themselves an exotic trophy.
31. CYBERSWITCH
First aired: 12/18/96
Summary: Jeremiah Surd switches bodies with Race, and goes after the only person who can reverse the process -- Benton Quest.
32. UNDERSEA URGENCY
First aired: 12/19/96
Summary: A seaquake releases a horde of murderous amphibians on a nearly-completed underwater research facility.
33. NEMESIS
First aired: 12/20/96
Notes: First appearance of Dr. Zin (in this series).
Summary: The nefarious Dr. Zin subverts a satellite designed by Benton Quest and uses it to hold the world for ransom.
34. DNA DOOMSDAY
First aired: 12/23/96
Summary: A bio-computer goes out of control during a simulation to test a military installation's defenses.
35. GHOST QUEST
First aired: 12/25/96
Notes: Yes, this episode contains the infamous kiss . . .
Summary: En route to Nova Scotia in the newly christened Questor II, Jonny, Jessie and Hadji come upon a fog-enveloped island with a tragic history.
36. NUCLEAR NETHERWORLD
First aired: 12/26/96
Notes: "Grandpa Doug" was named after original JQ creator, Doug Wildey.
Summary: While visiting Jonny's Grandpa Doug Wildey on his ranch, Jonny and Hadji find out that a nearby biodome experiment is actually a cover for a plant making weapons-grade uranium.
37. ECLIPSE
First aired: 12/27/96
Summary: A beautiful girl whom Hadji rescues in New Orleans exerts a strange influence over him.
38. WITHOUT A TRACE
First aired: 12/30/96
Summary: Air Force One vanishes, and all the evidence points to Benton Quest and Race Bannon. Jonny, Jessie and Hadji must elude government agents to prove their fathers' innocence, find the real culprit, and rescue the President.
39. VILLAGE OF THE DOOMED
First aired: 12/31/96
Notes: This episode was based, in part, on a British 60s sci-fi series called "The Prisoner"
Summary: Benton and Jonny head across the big pond for some fishing and father-son bonding in Devon -- and come across an idyllic little village that's just a little too peaceful.
40. TO BARDO AND BACK
First aired: 1/2/97
Summary: The Quest team employs QuestWorld to try and revive Race, who has been rendered comatose in a rodeo accident caused by Jeremiah Surd -- who in turn exploits the opportunity to attack Race at his most vulnerable.
41. DARK SENTINEL
First aired: 2/10/97
Summary: In Cameroon to help a scientist harvest life-giving sap from trees threatened by a logging operation, the Quest team finds that the locals are more than a match for the loggers.
42. OTHER SPACE
First aired: 2/11/97
Summary: Scientists working on transdimensional technology open a portal to another dimension - and its denizens, who waste no time staking their claim on Earth.
43. DIGITAL DOUBLECROSS
First aired: 2/12/97
Summary: Jonny and Jessie challenge each other to a VR game in Questworld -- but Surd has a challenge of his own in store for them.
44. THOUGHTSCAPE
First aired: 2/13/97
Summary: Jonny and Benton venture into Jessie's mind to undo Surd's malicious attempt to strike at the Quest team from within - but it turns out that Jessie can take care of herself.
45. THE BANGALORE FALCON
First aired: 2/14/97
Summary: While touring Bangalore, Jonny, Jessie and Hadji find a rare falcon, reputedly from a hidden realm that appears once every 500 years - a realm whose river's water is said to bestow immortality. A beautiful ornithologist is also very interested in the bird; but is she who she says she is?
46. DIAMONDS AND JADE
First aired: 3/15/97
Notes: First appearance of "Jezebel" Jade (in this series).
Summary: Race, Jonny and Jessie travel to Indonesia to help a certain old friend recover a precious jewel - which seems to be protected by a supernatural force.
47. THE EDGE OF YESTERDAY
First aired: 3/17/97
Notes: Last appearance of Ezekiel Rage (as far as we know).
Summary: Ezekiel Rage tries to destroy the world - again - this time by planting a nuclear bomb in the bowels of the earth. Jonny and Jessie must go back in time to stop him.
48. THE HAUNTED SONATA
First aired: 3/18/97
Summary: On a visit to the Czech Republic, Jonny and Jessie encounter a ghostly apparition that leads them to an incomplete sonata -- and a generations-old secret.
49. GENERAL WINTER
First aired: 3/26/97
Summary: General Vostok returns, this time armed with the weapon that defeated Napoleon. And he wants Benton to make it bigger and meaner.
50. NIGHT OF THE ZINJA
First aired: 4/14/97
Summary: The daughters of Zin are determined to carry on the Zin dynasty after their father's death (yes, you read that right) -- and their first target is the Quest team.
51. THE ROBOT SPIES
First aired: 4/15/97
Notes: Last appearance of the Rockport compound????
Summary: Dr Zin launches the ultimate plan to defeat the Quests, but this time Benton's had quite enough.
52. MORE THAN ZERO
First aired: 4/16/97
Notes: Due to yet another brilliant continuity error, "More Than Zero" aired after "The Robot Spies" which was, quite obviously, supposed to be the end of the season/series.
Summary: Benton, Jonny, Hadji and Race travel to Venice to investigate a haunted house. That's it.