I got filled with manic creative energy and had to finish the storyboards, here's the rest of the script:
Back in Knothole city another explosion rocks the base, Nicole looks terrified at Shard's gem as the vibrations threaten to destabilize the delicate crystal (perhaps shard notices a small glitch while fighting alongside Sonic, realizing he's living on borrowed time.) Shard and Sonic press their attack using coordinated moves that overwhelm Silver Sonic 3, forcing Metal to reboot into a body in the base to assist. What follows is an epic 2 on 2 battle which has the team of Sonic and Shard on the back foot until Shard realizes he can take a page from Metal's playbook, telling Sonic to make a dash towards the computer he charges Metal and slams him into Silver 3, activating his own self-destruct, taking all three of them out and giving Sonic the chance he needs to destroy the Metal Sonic backup system. Outside Eggman's base one of the Metal Sonic's in the kamikaze queue wakes up, its expressionless face nonetheless giving an impression of terror as it looks towards Metropolis, seeing the building housing his backup system explode as Sonic makes his escape. Metal twitches, instinctively moving to confront Sonic, but hesitating when he realizes he no longer has infinite lives.
Sonic returns to freedom HQ to see they're already working on a new body for Shard, who is talking from a computer monitor. The poetic irony is felt by all now that it's Shard who is housed safe at home while he remote operates his own body and now Metal Sonic only has one life to live.
*This is my interpretation of how we could keep both Shard and Metal in Archie continuity without feature creep or escalation. Shard is nerfed without access to the power gem, but is still around to help as a regular team member and be Nicole's love interest (because that is SUPER sweet and fuck you if you want to break that up) while Metal Sonic is brought closer to his video game counterpart, Eggman's most powerful creation, but without the option of simply reloading into a new and improved body after every loss like he's some kind of one drone Borg Collective.