Archie Sonic the Hedgehog Issue 99 was the ninety-ninth issue of the main Sonic the Hedgehog comic series.
- "Blow By Blow"
Sonic and Tails sneak in through the window late at night. Unfortunately for them, they wake up Bernie and Jules. Jules begins to lecture Sonic out he snuck out last night and that Tails has been missing since yesterday. Jules tells Tails that even though he isn't their son, they consider him Sonic's little brother. Bernie asks that they want to know about what's been going on.
Next morning, the Mobians cheer for King Max, Queen Alicia Acorn, Sally and Elias while chanting "All hail the House of Acorn". Sally in her thoughts is happy to have her family and a peaceful kingdom but is disappointed with her losing contact with her friends. Geoffrey St. John and the Secret Service arrive with bad news to report to Sally and Elias. At Sonic's house, Bernie and Jules discuss about Sonic being captured by Overlanders to battle a creature named "Shadow" (STH:98), and Tails whisked away by Athair to try to aid Knuckles. Mina arrives at the hedgehog home hoping to see Sonic, in which Bernie and Jules wake up Sonic to tell him.
At Castle Acorn, Nate Morgan reports Sir Charles' full message to Elias. Geoffrey tells Elias that they failed to retrieve the Sword of Acorns and they found Overlanders in Robotropolis. Nate Morgan tells Elias that Uma Arachnis stole the sword from Dr. Robotnik. Sally saying that Kodos is Arachnis' ally, so he may know where she is. Geoffrey and the Secret Service leave to interrogate Kodos. Elias looks at his mum and dad thinking that the role for ruling the Kingdom belongs to Sally. Sally slips out of the castle and asks some ladies in the Castle to help disguise herself like them.
Sonic and Tails attempt to teach Mina about her speed. Sonic asking if that's as fast as she can go, Mina goes too much and crashes into a tree. Sonic sends Tails back home as he attends to Mina. Mina blames Sonic that its all his fault. She thought that they had so much in common, roboticized parents, speed but she is upset that he's better with speed. Sonic apoligizes that he was only teasing and that its all part of being a Freedom Fighter. Mina overexcited that Sonic said she has what it takes to be a Freedom Fighter kisses Sonic, as Sally and the ladies are approaching. Sally extremely disappointed walks away.
At Castle Acorn, Kodos escapes from the castle and knocks out Geoffrey and the Secret Service. Sally takes off her mouth piece while still wearing the costume and asks Doctor Quack to help the agents. Quack tells them that he's gon insane from the toxins in Robotropolis and that without medical treatment, he would've died. Nate Morgan shocked at this while Overlanders were in Robotropolis. Sally tells Rotor and Tails that she's going after Kodos, but Rotor thinks that they should get Sonic "like old times." Sally believes its too late and they set off.
Sally, Rotor and Tails split off to search as Sally continues to think about Sonic and Mina. Sally finds a weakened Arachnis on the floor, as Arachnis has something to tell her.As she is telling Sally useful information, Kodos has captured Tails and Rotor from behind. Nate Morgan reports to Sonic that Kodos has escaped and Sally, Rotor and Tails have gone after him. As Sonic runs off leaving Nate and Mina, he wonders why Sally didn't get him.
At Knothole Prison, Antoine looks at the High Sheriff upset about him still under Dr. Robotnik's control. Bunnie attempts to comfort him, but Sonic arrives that he needs their help. Sonic, Bunnie and Antoine give chase to stop Kodos and save the others.
- "What Comes Around Goes Around"
Chaos Knuckles has teleported to some ruins after hearing Julie-Su's voice. He wanders inside and sees her being captured by the Dark Legion...and himself coming to rescue her. The spirit of his Grandfather Hawking appears and tells him that his powers let him teleport across time as well as distance. To demonstrate, Hawking takes Knuckles to his dead body in Haven. He tells Knuckles that he is evolving.
The Dark Legion, led by Dimitri, is approaching the Floating Island and picking up the energy signals—one from the Island, the other from Chaos Knuckles. Knuckles' energy wave disappears suddenly. Dimitri begins to suspect what is happening and tells his assistant Lien-Da to recover her half sister Julie-Su from somewhere in the ship. Knuckles appears in the ship and Dimitri declares that they need to talk, to which Knuckles agrees.
- Sally witnesses Mina kissing Sonic and thinks they are a couple.
- Kodos escapes the castle, defeats Arachnis, Tails, and Rotor.
- Knuckles is revealed to be able to travel across time
- Dimitri and the Dark Legion return to the Floating Island.
- What happens in between this issue and the previous issue is eventually revealed in Sonic Universe #2, as the events of the previous issue and SU: #2 are based on the events of the videogame Sonic Adventure 2. SU: #2 completes the adaption.