Hey, I'm not sure if this was clear, but there was lots of time in between some of the events. (ie: The info Shadow gave Robotnik, Eggman's attack on the GUN base. ). So there was lots of free time with Sonic and Shadow, this allowing their relationship to grow.
Shadow could feel his chaos energy overflowing. He Chaos-Controlled to the house and appeared in the living room. "Woah! Shadow?! Shouldn't you be in the hospital?", Sonic questioned.
"I guess I had a chaos surge. I feel great!"
"Well, I'm happy to hear that. Hey Tails!"
"What?"
"Shadow's back! He says he had a chaos surge."
"That's great!" Shadow sat next to Sonic. "How did the expedition go?"
"I didn't find anything."
"Dammit. We have to find him soon."
"Don't worry about it Shads, Tails is working on it."
"Alright, I'll trust you." Sonic gave Shadow a small kiss, but, as usual, Shadow wasn't satisfied. He pinned Sonic to the couch. "You might wanna lock the door this time." Shadow groaned, and walked over to lock the door. He returned to Sonic, "Happy?"
"Very." Shadow climbed back on top of Sonic. Sonic liked being pinned under Shadow. It was cute to let Shadow have his way. He leaned down by Sonic and brushed his lips against Sonic's. He was teasing him again.
Project X walked into the laboratory. "Did it work?", Eggman questioned.
"Yes. Shadow is back on his feet. So, when am I actually going to get to fight him?"
"All in good time. You know, I might release you when I'm done, if you behave." Ivo was just as gullible as Gerald. Project X fully intended on ditching Eggman as soon as he got to Shadow.
Their tongues danced together in each others mouths. Shadow was the best, despite his lack of experience. Shadow pulled away, a small line of saliva going from his to Sonic's mouth. Sonic groaned in disapproval, wanting more. Shadow shut him up by giving him a small love bite on his neck. A small moan left Sonic's mouth. Shadow had hit the spot again. Shadow's hand traveled down Sonic's chest, going down below his waist. Sonic's eyes widened , "Not here Shadow." Shadow frowned. He picked up Sonic and carried him to their bedroom. He set him down on the bed. He shut the door behind him. Shadow had Sonic all to himself.