Disclaimer - I don't own the Sonic characters.
Hidden Happiness
He kept them buried where no one would ever look, or where he hoped no one would look. The spot was obvious, after all. Too obvious. So the chances of someone looking for them there had to be slim which made him feel safe.
Knuckles didn't know what he would do if someone ever found out.
He had made his secrets with his own hands. During one of the times the Master Emerald had been stolen, he'd stopped by a store and purchased the materials he needed, using the coins he dug up on Angel Island. Once the Master Emerald had been recovered, he set about making his three secrets. He spent hours sewing them together. When he was done, he had three miniature versions of the three people closest to him: Sonic, Tails, Amy. And then, for hours, he would play with his friends on the lonely island that was his home.
This, however, was blasphemy. As guardian of the Master Emerald, he needed no friends. He needed only his duty: protect the Master Emerald and its sacred land.
But he couldn't help himself, and so found himself playing with his dolls daily. That is, until he was almost caught. Tails, always curious about the unknown, often visited the island to ask if he could search through the ruins (sometimes he did so without permission). Knuckles always denied him his wish and sometimes pummeled the fox to get his point across, which would bring about Sonic coming to the island to pummel Knuckles, which resulted in Amy coming along because….well…Sonic was there.
But on the day he was almost found out, he'd been sitting with his back against the Master Emerald, engrossed in his world of make-believe. He didn't hear Tails' footfalls until the fox was nearly upon him. Scared witless at almost being found out, Knuckles tossed his toys behind him and leapt upon Tails before the fox could see anything and started the pummeling. Tails left the island, bruised and in tears. And Knuckles, forgetting about the fox cub, returned to his imaginary game.
He completely forgot about what always happened after he pummeled Tails. He barely had time to stuff the dolls behind his back when Sonic came rushing up to him. Momentarily distracted from his reason for setting foot on Angel Island, Sonic asked what Knuckles had hidden behind his back. Knuckles responded with his fist, sending Sonic several feet away from the Master Emerald with one mighty punch. Then running after Sonic, he proceeded with their fight, ultimately getting pummeled in the end.
Dragging himself back to the Master Emerald he returned to his imaginary pursuits, ignoring the pain of his injuries. That's when Amy showed up. He stuffed the dolls behind his back. Amy didn't seem to care what he hid. "Have you seen Sonic," she asked.
"No. Now get off my island before I throw you off." Because he had once, Amy hurried away.
That's when Knuckles knew he had to get rid of his dolls.
He decided on a burial for them and scoured his island, looking for the perfect place—one that wouldn't be dug up by curious foxes. In the end he settled on the most sacred spot, one that would be overlooked due to what rested upon it. He buried his dolls beneath the Master Emerald.
To this day, Knuckles stands guard over the Master Emerald, protecting it, the island, and his hidden friends.