What you recognize I don't own. What if in Treasure Planet Silver wasn't actually a pirate but a deep undercover agent for the Interstellar Navy?, Silver saw an opportunity to let the Navy know that he was still alive and on his mission, which is to catch pirates by pretending to be one himself. Due to how dangerous his mission is contact is sporadic, primarily through being on pirating missions, but if he can't catch pirates by being a pirate he does have other means of getting in contact with the Navy to let them know he's still alive. Treasure Planet was supposed to be his last mission but then he heard of a possible pirate crew that was even worse than the legends of Treasure Planet and so had to make his escape to catch that group before his replacement fully took over, and no one knew who he really was by the way

When Silver first came on board the ship he instantly recognized Captain Amelia but also knew that she wouldn't recognize him or his mission and so simply acted like a normal crew member until the time was right to strike. When Scroop killed the first mate he had a confrontation immediately

"Scroop I thought I said no killing"

"I felt it was necessary, and blaming the boy was easy too"

"Well until I say so no more killing, we need these people alive to get to the treasure understood?"

"Yes sir"

Silver went to his assigned cabin and then spoke to himself like he always did

"Days like this are the hardest ones for me, I think it's finally time to retire from field work for a bit and return home, at least they'll know I'm alive when they see the crew list for Amelia's ship. I wonder how long it's been this time around since they last heard from me via my name showing up on a pirate mission, though at least they learned their lesson after last time a ship blew up on me"

Silver decides to keep the pirates on a tighter leash acting like the Captain of the pirates when in reality he didn't want to have any more casualties. Shortly before they arrived on Treasure Planet Silver overheard talk of an even more dangerous group after a more dangerous treasure than Treasure Planet

"Right guess I know what my next mission is, so much for leaving this pirate life behind after Treasure Planet"

He quickly gets back into the mindset of being a pirate after Treasure Planet though since that was his current mission he also made sure to keep a detailed report and knew where to hide it so that it would be given to his superior's at the same time Captain Amelia's was made so that they knew he was still alive and where he was going next

"Right then, time to continue the mission"

And so thought it took careful planning the mission ended successfully and he managed to escape the ship taking him home on pirate charges to continue his mission. Once Silver left he wondered around for several months before finally making it to his goal of the group that was even worse than Captain Flint and the loot of Treasure Planet

"I be wanting to join your crew"

"What can you do?"

"I can cook"

"Fine"

For three years Silver tried to find an opportunity to get the group, along with himself, captured but doesn't succeed until a slightly older Jim Hawkins came across his path as a cadet

"I can't let you go again Silver, I'm a soldier now, or well I will be once I graduate from the academy"

"I know Jimbo, and honestly I don't mind being taken in, it's time to go home"

"Huh?"

"You'll see Jimbo, you'll see"

Three weeks later and Jim does indeed find out what Silver meant, because during the trial Silver is identified as part of the Interstellar Navy deep undercover to catch pirates. Once things were resolved Silver was given two choices, either the chance to retire or to become an Admiral commanding the fleet from a desk. Silver was also given time off to truly think about the decision ultimately deciding to retire, he had thought about becoming an Admiral and had honestly come close to choosing that option but realized that he was tired, too tired and old to continue serving the military. However on occasion he would help Captain Amelia on the Legacy for short supply runs if she happened to be short a crew member, and also just went sailing occasionally for the fun of it. As for Jim he would graduate with honors and serve the Navy with dignity, ultimately getting his own command at a relatively young age, when he found out about Silver's death during a run on the Legacy (Silver had died like Arrow had, his line hadn't been properly secured deliberately by a traitor during a war with another group) he mourned his loss and managed to get time to attend Silver's funeral which had been with honors. He would dedicate the rest of his service in Silver's honor, and once he retired he told stories about Treasure Planet and the pirate who wasn't actually a pirate until he died