Robotnik's Troopers are on the warpath, arresting Emerald Hill Zone resident Amy Rose for associating with Sonic the Hedgehog, which is a criminal offence. Johnny Lightfoot and Bob Beaky are watching, Bob knowing that Sonic won't be happy when he hears Amy's been saying she's Sonic's girlfriend again. Johnny dresses for action and Bob casts away his heavy coverings, revealing Sonic, and the heroes charge into battle. The Troopers fire Weapon X, which misses Johnny and Sonic, but fires off a torrent of spikes in the resulting explosions, seriously endangering the Emerald Hill folk. Just as Sonic grabs all the spikes, only just rescuing young Cedric, the Troopers' ship warps back to Robotnik's base in the Special Zone. Now Sonic and Johnny are the only ones who can rescue Amy (though the hedgehog isn't happy about the idea one bit).
In Robotnik's Egg Fortress in the Special Zone, the dictator is meeting with image consultants Thomas & Miller, who have planned an image change for him. He doesn't care if his 'subjects' like him or not, but agrees (upon turfing the pair out) that his body has served its purpose and needs a change. Robotnik's chief scientist, Grimer pops in and is surprised to find that his master has literally encased himself in a giant egg. Back on Mobius, Sonic and Johnny enter their base in Kintobor's Laboratory, where the Kintobor Computer informs Sonic of where Amy is. Sonic activates the team's Star Post and he and Johnny soon arrive in the Special Zone and make their way to the Egg Fortress. Sonic breaks in, and he and Johnny quickly encounter the Fortress' automatic defences and are quickly encased in a giant bubble. Grimer and a pair of Troopers arrive to deal with the intruders, the scientist smirking, saying that Robotnik can't be available to greet them as he's changing, just as the dictator's egg ominously cracks.
Robotnik bursts out of his egg in a new form, feeling 'more rotten than ever.' In a laboratory elsewhere, Grimer gloats over his prisoners, annoying Sonic in sharing Amy's belief of the hedgehogs being in love. The reborn Robotnik bursts in and tells the imprisoned heroes exactly what he plans to do with them: convert all three into new Super Badniks. As Amy is placed in her Badnik suit, Sonic and Johnny push their bubble prison out of the basket it has been sitting in and attack the Troopers. One remaining Trooper points a gun at the bubble, ignoring Grimer's order not to shoot, thus freeing the heroes. As Johnny recovers, the heroes hear Amy screaming within her suit, feeling the Badnik program trying to take over her mind. Sonic, after a second's consideration, spin-attacks the Badnik, freeing Amy, and retreats with Amy and Johnny.
Robotnik roars for someone to stop the fleeing heroes, only to find Grimer smashing the last Trooper. Enraged that Grimer's destroyed the only available Badnik that could catch Sonic, the dictator promises an unpleasant punishment for his scientist.... Back on Mobius, the Freedom Fighters have no option but to let Amy, who is no longer safe in the village, join them. Sonic reluctantly agrees, but wants Amy to know that she isn't his girlfriend. Amy remains confident that things will go her way, however. Meanwhile, Grimer and Robotnik are putting the finishing touches on their next weapon: Project Metallix!
- Robotnik's design change was not universally praised - at least one Boomer wrote a letter of complaint, which was published in a future edition of Speedlines.
- Johnny grows somewhat when he puts clothes on.
- The concept of a Super Badnik would be revisited later in the comic's run with the introduction of Shortfuse.
- Nigel Kitching originally based Amy on 1930s/40s Hollywood "screwball comedies" but this was quickly dropped, as editor Deborah Tate wanted Amy to be a more mature character. Even by the next strip though, Amy is suddenly showing flashes of maturity and competence that are missing in Girl Trouble.
- Amy continues to lie that she's dating Sonic even when the Troopers are dragging her off.
- Robotnik's image consultants are also humans. Where they came from is never explained.
As part of Issue 261's 20th anniversary celebrations, the events of "Girl Trouble" were altered slightly to include time travel. Rather than appearing straight in the Special Zone via Star Post, Sonic and Johnny arrive in a 2013 Metropolis Zone through a portal, face to face with a future Sonic and Tails. There, Johnny accidentally learns that he dies in the near future but agrees to never again talk about this episode.