I hadda go look some stuff up to do this, cause I couldn't remember all the inconsequential junky stories in between the Sonic 3 adaptation and the Sonic and Knuckles adaptation, but here we go. ^^
Issue #39 featured the one-shot "Sonic No More," which saw Grimer use a device stolen from the deceased Mobian physicist, Professor Neinstein, to transfer Sonic's superpowers into Robotnik. Sonic reverted to the way he looked before he broke the sound barrier, and Robotnik got blue and fast. They fought, Sonic ran, they fought again, but then, when Robotnik commanded some Badniks to attack Sonic, they turned on him, as he matched Sonic's parameters. Grimer quickly removed Sonic's powers from Robotnik to save him, and Sonic, restored, smashed the device. This issue contained a notable mistake - it portrayed the Freedom Fighters as still operating out of their underground base, which Robotnik destroyed in the previous issue.
Issue #40 was another one-shot, considered, from what I've read on here, to be the worst Sonic story of all - "The Frozen Zone." Sonic and crew headed to the Frozen Zone for reasons totally unexplained, and we saw that it wasn't actually the tundra we'd seen of it before, but had previously been a happy little place that had been frozen solid, inhabitants and all (seems Sonic and crew came here because of this, but, y'know, they've been to the zone before...). Long story short, it was some nutcase human with no explanation called the Chiller, using his Chill-Bots, Chill-Guns and Chill-Machine. Obsessive much? Sonic beat him, he turned nice, the end. Load of old [censored].
The icy theme continued over the next two larger-sized issues, with "Ice Cap Attack!" After a portal opened to unleash a Badnik attack on the Emerald Hill Zone, Sonic leapt back through it and wound up in the Ice Cap Zone on the Floating Island, which Robotnik is using for a staging ground. Sonic and Knuckles are unwillingly forced to team up to take Robotnik down, and after they do so, Knuckles warns Sonic not to come back.
Another two-parter was in issues 43-44, "Badnik's Bridge," as the Freedom Fighters had to stop the transport of the new main thrust for the Death Egg to it's repair site on the Floating Island. They blow up a bridge, yawn. Story's notable for introducing the SBS, Special Badnik Service, specially modified Trooper Badniks.
Next was " Day of the Death Egg." It appeared that the Death Egg launched and attacked the Emerald Hill Zone, wiping out everything - but, oh no, s'okay, it was just a video simulation Grimer whipped up. But they've just taken delivery of the new thruster...
Now, you might ask yourself, what were Kitching and Elson up to prior to Kitching's return with "Badnik's Bridge," and Elson's with this story? Well, they were busy with another strip in the comic - Knuckles's first series, "Carnival Night Conspiracy," which started in the same issue as "Sonic No More," right after Knuckles left the Freedom Fighters at the end of "Robotnik's Revenge" to return to the Floating Island. When he did, he discovered that the Marxio Brothers (from #18-19) were there running Robotnik's latest enterprise, the Carnival Night Zone. He's not best pleased that they've brought this tacky place to his island, but they manage to persuade him it's a good idea, then try and off him with dangerous rides and the like. He doesn't take kindly to that, and [censored]ters a fault line near the Zone, smashing it clean off the Floating Island. This story wrapped up in #44, the issue before " Day of the Death Egg."
Next Sonic story was another one-shot, "The Big Con." A convention was being held by Doctor Robotnik in the Chemical Plant Zone, but the centre was actually a Badnik processing plant. Sonic and crew are in attendance, blow up the place, go home, that's it.
The following issue, joyously, was the beginning of the adaptation of "Sonic and Knuckles," beginning with the two-part "Mystery of the Sandopolis Zone" (#47-48). Sonic heads to the Floating Island once again to take out the Death Egg, but as he approaches via the Sandopolis Zone, he runs into Knuckles, who is not happy to see him.
(Continuity error - Knuckles claims he told Sonic never to come back to the Floating Island, which he did during "Ice Cap Attack." But when Sonic asks why he hasn't done anything about the Death Egg, Knuckles says it's because he was held up with the Marxios. But if Knuckles is only coming to the Death Egg now - hence, has only just finished with the Marxios - and he ran into the Marxios immediately after returning to the island... when the heck did "Ice Cap Attack" take place?)
Anyway, Sonic gets attacked by a Badnik and Knuckles saves him, and they once again agree to uneasily team up. But who should they run into... why, Captain Plunder? He's accuquired a map that will lead him to the lost pyramid of Sandopolis, and the treasures within it. The buried pyramid is raised, but it has a defender, a massive stone guardian that reassembles himself when Sonic smashes him. While S&K struggle with the guardian, Plunder and co. head into the pyramid. Knuckles tricks the guardian into walking into quicksand, but Plunder and co. have their own problems when angry ghosts chase them out of the pyramid. S&K however, get stuck inside, and Knuckles breaks a seal to allow sand to pour in and submerge the pyramid again. Knuckles then leads Sonic out through a series of tunnels.
(Another error - in this story, Filch is unable to help gather treasure because "he's a ghost," and hence can't touch anything. However, in the very next issue, when Captain Plunder's own strip starts, he opens a vault from the inside, and we're clearly told he's a poltergeist - "one of them ghosts what can move things" ).
S&K emerge from the tunnels into the Lava Reef Zone, and discover they're right under the Death Egg, which is perched atop a volcano. They are attacked by EggRobo Badniks, but Knuckles takes them out by giving them a lava bath. Knuckles leads them to the nearby Chaos Emerald chamber, where Sonic marvels at the size the now-fully-powered emeralds have grown to... but they are not alone in the chamber, and are confronted by... Metallix, the Metal Sonic! ("Countdown to Disaster," Part 1, #49)
This new model Metallix, drawing power from the Master Emerald, escapes via a teleporter to the Sky Sanctuary, taking the Master Emerald with him. S&K pursue, but Knuckles is taken down in one punch. As Sonic struggles with the Metallix, it reveals that it and the previous Metallix are only singular members of a greater, elite brotherhood. A punch hurls Sonic on the Master Emerald, and he warns Metallix - "You're not the only one who can get a buzz offa this thing!" The chaos energy transforms Sonic into Super Sonic, and he promptly punches Metallix's head off and rips him to bits. He then turns on Knuckles, beating him senseless until he turns back to normal... but when the duo turn to look for it, the Master Emerald is gone... and the Death Egg has launched! ("Countdown to Disaster," Part 2, #50)
(Side note: even when I was younger reading this, the poor handling of time travel chaffed my butt. The original Metallix was *erased from history.* No-one - except maybe Sonic, as he was the time-traveller - should remember him, and I'm not entirely sure that more of them should exist in the first place. However, I grew quite willing to just ignore it, 'cause we got the awesome Brotherhood of Metallix stories out of it.
)
The Sky Sanctuary begins crumbling, and Knuckles, with Sonic on his back, glides toward the Death Egg, now being powered by the Master Emerald. Avoiding the fire of some EggRobos, Sonic smashes his way in, as Knuckles heads back to the island with a plan. As Sonic battle some Spikebonker Badniks, Knuckles activates an ancient mechanism beneath the surface of the Floating Island... and it begins to move... (" Disaster!" Part 1, #51)
Sonic has been captured by the Spikebonkers and brought before Robotnik, but as Grimer targets the craft's disintegrator beams on the Emerald Hill Zone, Knuckles attacks by activating a weapons system with the Floating Island, which blasts electricity at the Death Egg. The Death Egg retaliates, blasting at the island, but then Sonic knocks the Master Emerald out of the reactor, shutting off the Death Egg's power. Another blast from the Floating Island rocks the Death Egg, and Sonic, the emerald, and a swarm of EggRobos all spill out through one of the craft's [censored]tered eyes, and begin the fall back down to Mobius. (" Disaster!" Part 2, #52)
It's all over for the Death Egg, but it's still a long way down for Sonic, who snatches an EggRobo's gun to stop another of the Badniks from nabbing the Master Emerald. The Emerald falls onto the Floating Island, and Sonic snags a jetpack from another EggRobo and jets over there to find it. Unfortunately, Robotnik has abandoned the crippled Death Egg, and is waiting for him in a new battle suit. Sonic cuts loose, utterly destroying the suit, to Robotnik's shock, and forcing him off the island's edge. His damaged jets take him down safely... but not softly. Sonic retreives the emerald, as Knuckles comes running up, intent on returning it to the chamber before the island falls. But Sonic wants a little favour in return for handing it over... the populous of the Emerald Hill Zone must be allowed to evacuate onto the island's Mushroom Hill Zone, where they can live in safety. Knuckles agrees, and the emerald is returned and the inhabitants moved... but Robotnik swears revenge. (" Disaster!" Part 3, #53)
This would lead to another chain of (Stringer?) fill-ins between the next big Kitching/Elson arc, while K&E worked on the next Knuckles story, "Total Chaotix," which began in this same issue, #53. But that's for another time, because my hands hurt. ^^;