The heroes arrive at Mario's house when Mario transforms into Dr. Mario and helps Princess Peach with nursing Yoshi. Yoshi wakes up but is still immobilized. Sonic and Luigi are still mourning over the incident and Shadow talks about how everyone was stupid and played a role in failing. Professor E. Gadd then shows up and talks to the heroes and says that he has been researching more on the Chaos Emeralds. He said that it reveals Key Elements that nobody knew about. Sonic then questions him as he explains. Professor E. Gadd says that he was researching and tapped into the Chaos Emerald the heroes had's energy and saw what it was really capable of doing.
Then, he said that if one is to collect all 7, they could unlock the Key Elements within its hidden powers. Shadow then demands that instead of talking they go get more Emeralds. Sonic then gets the Emerald back and as they are soon about to head out, a flash happens and the Chaos Emerald disappears. Everyone is shocked and Shadow says that they are idiots. Professor E. Gadd then asks them to retrieve the Chaos Emerald back. The heroes except and then get ready to head out. Shadow storms out as Mario and Sonic try to stop him. Mario and Luigi then transform into Cape Mario and Cape Luigi.
They then head to Goomba Fields. At Goomba Fields they see that there are four Metal Sonics as the Metal Sonic Bros. As they were going for a sneak attack, Shadow ruins it by confronting the Metal Sonic Bros. himself. The heroes then come out of hiding and the Metal Sonic Bros introduce themselves twice. Shadoe gets annoyed and goes to attack the leader. However, the other Metal Sonics stop him and the leader kicks him to the wall. Shadow emerges fromt the wall but is luckily stopped by Sonic. The Metal Sonic Bros. then say that they are the ones who defeated Mecha Sonic. They all prepare to fight as Mario takes on metal sonic #1. They are equaled until Mario kicks him to the ground. He then arises and punches Mario. Mario gains mobility and pounces Metal Sonic #1 using the wall. He then smashes him through the wall and jumps through. Shadow then takes #2 and Luigi gets hit by #4.
Sonic and Metal Sonic #3 then battle it out. Metal Sonic #3 then beats up Sonic, then Sonic counters and uses his Hurricane Kick and kicks him down. Metal Sonic #4 tries to find Luigi but can't. Cape Luigi then smashes him into a wall with his hammer. Metal Sonic #3 then kicks Luigi and Sonic comes down to help him. Shadow then kicks Metal Sonic #2 and then uses a combo on him and then kicks him up. Mario crashes into him, followed by Metal Sonic #1. Cape Mario then beats both up with his hammer. Metal Sonic #3 then punches Cape Luigi followed by Metal Sonic #4 and they both try to kick him until Sonic uses his Hurricane Kick on Metal Sonic #3 and hits him up.
Cape Luigi then uses his Spin Attack and then hits Metal Sonic #4 up. Sonic and Cape Luigi then combo on Metal Sonic#3 until Luigi uses his Luigi Headbutt. Cape Mario flies Shadow and then throws him at Metal Sonic #2. Cape MArio then fights MEtal Sonic #1 as they go back to back but Cape Mario punches him and kicks him to the ground where; Cape Mario, Shadow, and the first two Metal Sonics go head on. Soon Shadow and Cape Mario get the final punch and all the Metal Sonic regroup. They then use the Chaos Emerald they possess to go into Semi-Mecha Sonics. They then use their Heavy Ball Bomber and defeat Mario, Luigi, Sonic, and Shadow. They then take everything the heroes have and leave. The heroes just lay fainted as the Metal Sonic Bros. continues their reign of terror.