What happened to metal sonic at the end of sonic heroes

This is uncertain. Metal Sonic is last seen in Sonic Heroes after he deactivates upon being defeated. He is picked up at the end by E-123 Omega, who exchanges a glance with Shadow. But, no further reference is made to him in the next game in the main series, Shadow the Hedgehog. Therefore, it is probable that Omega didn't keep him. Several things then are possible:

• He is destroyed by Omega and/or Shadow. Omega would do it to prove that he is the strongest of all Eggman's robots and Shadow might do it out of revenge. The Chaos Emeralds, which had the power to return Shadow's memories, were instead used by Sonic to turn into his super form to stop Metal Sonic/Neo Metal Sonic/Metal Madness/Metal Overlord. It is possible that Shadow thought that he could do this without the aid of the Emeralds. If he could, then he could have used the emeralds to restore his memory. Shadow has less of a motive, though.
• He is left on the Airship, which is subsequently scrapped. The Armada is never seen of again, so Eggman probably just destroyed it or recycled it. In this process he could have either destroyed or found Metal.
• Eggman found him after Escaping the Chaotix. This could tie in with the above, but it is possible on its own. Eggman would probably just reprogram his creation and ready him for use again.

Metal Sonic makes appearances afterwards in the Sonic Rivals series. However, these games may not be canon, as they are on the handheld sereis (which could split after Sonic Adventure 2, but still have key events of other games). Overall, it is probable that Metal Sonic survived, and is now in the possession of his creator, Doctor Eggman.