Machenstein, on 01 December 2014 - 01:07 PM, said:
Fang was trying to sell the Emeralds to the highest bidder, Robotnik put in a bid but Sonic made off with them before the deal could go through. When Knuckles went to collect, no emeralds, angry Echidna, crafty weasel-wolf with nifty toys and an irritated Robotnik sending Badniks to go pick up a now trapped Knuckles because he doesn't know where that big energy source on Angel Island is centralized and it would be easier to trace Knuckles going to it. Sonic just arrived before Robotnik could get him out the cage. Since the plan was over, they shook hands to make both a truce and to show respect to one another before leaving the base.
Because this is purely speculation on the timeline, I'll add in some fanon in that the Atomic Destroyer is the same weapon as the two in the Death Egg's eyes, but the one in the game is being constructed off Angel Island to replace one of the damaged ones on the Death Egg. Robotnik doesn't want Knuckles getting jumpy with a weapons construction on his island with the chance of it going bang and taking out a chunk of the island. It is designed as an improvement over a design Robotnik managed to get from Gerald's Diary after hacking G.U.N, the design being a successor to the Eclipse Cannon that was never constructed as it was still under consideration by G.U.N. when they assaulted the ARK. Again, this part is fanon, you can ignore it and nothing really changes.

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