Storyline
With the exception of issues 25 and 29 the series was broken down into three part story-arcs:
The Dark Legion
Led by Kragok, The Dark Legion, a cult of technology-worshiping echidnas formed by the disgruntled son of Enerjak, return from the twilight Zone that Steppenwolf, the second Guardian, sent them too so as to reclaim the Floating Island. Knuckles and the Chaotix defeat them as their plan is about to succeed destroying their base. From this story to present the Dark Legion have been hiding/living on the Floating Island. The story also re-accounted the history of the Dark Legion and the history of Steppenwolf, the first fully trained Guardian.
Lost Paradise (Issues 4-6)
The damage caused to the Zones (alternate realities) in the Endgame story-arc in the regular Sonic the Hedgehog series causes Echinopolis (the capital of the Floating Island) and Echidna's ancient enemies the Dingos to both return to the Floating Island after they were evacuated to The Hyper Zone by Guardian Hawking some 200 years earlier to escape the radioactive fallout of a Dingo missile strike. But both cities are attempting to return to the same location which could cause them both to be destroyed. Knuckles meets his mother and Julie-Su, and deals with the warring General Stryker. Echidnapolis is the city that survives, leaving the Dingos stranded there and causing a housing problem. The story also told the history of the disappearance of the Echidnas and introduced Constable Remmington and Grandfather Hawking.
Dark Vengeance (Issues 7-9)
Mammoth Mogul revives Enerjak from his space prison and returns him to The Dark Legion (after quickly defeating the fire ants), and the Chaotix Enerjak tortures Knuckles for an entire issue before splitting him up into individual molecules and leading his Dark Legion to Echinopolis where he clashes with the Dingo and Echidna armed forces, a fight which lasts until Mammoth Mogul appears and drains Enerjak of the energies he absorbed from the Chaos Emeralds, leaving him an old man. The story continued onto Sonic the Hedgehog issue 56 where Super Sonic, Hyper Knuckles and Turbo Tails fought Mammoth Mogul. Julie-Su also went undercover into the Dark Legion in this story causing readers and characters to question where her loyalties lie (either her old cult or Knuckles and the Chaotix).
The Lost Tribe (Issues 10-12)
Introducing yet more Echidnas, The Lost Tribe are the descendants of the Echidnas who chose to stay on Mobius when the Floating Island was raised they are currently under the leadership of Athair, Knuckles' ancestor who abandoned his role as Guardian to lead them. Knuckles is left in charge of the band after Athair vanishes and safely takes them to Albion via Mercia which is under the rule of Antoine D'Coolette's robotisized father. The story ties into Sonic the Hedgehog #59 and introduces Rob O' The Hedge and also tells the origin of Athair.
The Chaotix Caper (Issues 13-15)
A story focusing on The Chaotix, which now include Julie-Su. The team are caught up between two warring gangsters—Renfield The Rat and Downtown Ebony Hare. Hare was worried about Renfield's new Happyland amusement park because of its 'Special Sauce' -- an addictive drug the rat put in the food. The 'Special Sauce' seems to be especially poisonous to bees and kills Charmy's childhood friend Mello and nearly kills Charmy, who has to be operated on. Julie Su also nearly perishes when she discovers what is going on and is thrown from a roof by Hare while the Chaotix are recovering in hospital from the Special Sauce. After recovering and stopping Hare the Chaotix bury Mello and Charmy reclaims his birthright as prince of the Bees. The story tells Charmy's origin and also reveals that he can grow to 'normal size' as well as the small size he was shown as being previously. It also introduced Harry the Cabbie.
Reunion/Deep Cover (Issues 16-18)
Fully introducing and focusing on the Brotherhood of Guardians. One of their number Tobor was replaced by Moritori Rex the father of current Dark Legion leader Krygok after a battle between them left them both blind and buried in rubble. The real Tobor returned to the Floating Island and his revelations lead to a battle between Knuckles and Krygok, and then Tobor and Krygok leading to the latter two being trapped in the Zone. Their fates have never been addressed. The story introduced a strange reaction caused by the meetings of the Descendants of Dimitri (The Legion leaders) and the Descendants of Edmund (The Guardians) that opens portals to other Zones.
The Forbidden Zone (Issues 19-21)
A crossover with the Sonic the Hedgehog series, the story follows Knuckles and King Acorn's Secret Service#Members#Geoffrey St. John|Geoffrey St. John's King Acorn's Secret Service|Secret Service as they journey into the Forbidden Zone (the location of Haven, the base of operations for the Brotherhood of Guardians). The Secret Service are looking for Queen Alicia and Knuckles is searching for answers about his past, and they are both shocked to find Prince Elias, an heir to the Acorn throne nobody had previously known about. This story, though lacking much in the way of action or adventure would have huge ramifications in the Sonic the Hedgehog series.
Dark Alliance (Issues 22-24)
The Dark Legion tries to gain control of the Floating Island via an upcoming election in Echidnopolois, taking control of a prominent senator to support their Hitler-like candidate Benedict who soon gains the public's favor. Enerjak, now powerless and a cyborg, takes control of Haven and kidnaps Knuckles, Julie-Su, General Stryker, and the Brotherhood of Guardians. They are freed by Locke and Spectre, Benedict is revealed as a robot and the Legion escapes once more. This story also introduced Lien-Da, who has gone on to become a major antagonist in Sonic the Hedgehog. Also notable in this story was Benedict's mention of a secret held by Constable Remington, an issue not seemingly resolved until much later in the main Sonic the Hedgehog title.
Issue 25 detailed Knuckles' origin and his meeting with his father for the first time since he abandoned him as a child.
The First Date (Issues 26-28)
A story focusing on Knuckles and Julie-Su's friendship. When Julie-Su goes out on a date with another Echidna, Knuckles finds out the date clashes with a surprise party for Knuckles' birthday.
A Friend in Need (Issues 26-28)
A back-up story featuring Mighty the Armadillo, adapting the arcade game SegaSonic the Hedgehog. Mighty and Nic the Weasel rescue Ray the Flying Squirrel who has been trapped holding onto a gem since Sonic and Mighty escaped from a prison camp years earlier.
Issue 29 tells a story of when Princess Sally Acorn used to vacation on the Floating Island and play with Knuckles.
King of the Hill (Issues 30-32)
Monk, a purple ape who bullied Knuckles as a child, returns to the Floating Island after being literally thrown off the Island by The Brotherhood of Guardians. Their fight is interrupted by the Overlander Hunter, who hunts Mobians for sport. Fitted with restraining collars the two are forced to work together to evade Hunter using Knuckles' knowledge of the Island and Monk's brute strength. Knuckles releases the full force of his Chaos Emerald-born powers to stop Hunter, who is, as a result, imprisoned by The Brotherhood.
Though the series was canceled with issue 32, Penders resolved many dangling plot threads in Sonic Super Special #14. He also continued to write back-up stories in the regular Sonic the Hedgehog series that followed the ongoing series in which Knuckles developed fully the Chaos Emerald based powers he first displayed in the King of the Hill story-line. Knuckles eventually died to save Enerjak's life. The Afterlife story that followed was part of the lead up to Sonic the Hedgehog #125 and following the 1-year jump in issue 130, Knuckles and The Chaotix were living in Knothole City working as Freedom Fighters.
Most of the characters from the ongoing series were dealt with in the Return to Angel Island story-line (issues 138-141) where the Dingos had taken over the Island, the Dark Legion were acting as a resistance group, and the Brotherhood of Guardians were missing. Hunter, Constable Remington and the Fire Ants were among the casualties of the story-line, though the story also raised some questions as to the whereabouts of some of the Knuckles the Echidna characters, most notably General Stryker.
Read more about this topic: Knuckles The Echidna (comics)