Robotnik was inside his base preparing to send his badniks towards Sonic to hold him off and he sent Scratch and grounder against him leaving you, Robotnik and Metal Sonic to leave for the elevator but Exeller got through quickly.

Exeller: "Am I a joke to you Doctor?"

Exeller spin dashed at you three but Robotnik got a green ring which knocked Exeller back and Sonic was back in control long enough for them to escape as they got in the elevator...then it detached as you all landed down in the dungeon.

Robotnik: "That was weird...but now we must focus on escaping."

(So yeah Metal Sonic is now part of the team.)