Multiplus's shields doomed him. When Captain Marvel saw that some of the sea of endless duplicates were willingly jumping into the path of his lightning, he realized which one was the original, and made his move. 

Faster than the cloner could follow, he swooped down and grabbed him under his arms, flying up and away before Multiplus could even react. He got high enough that struggling would be a bad idea, and then shifted him around so that he was holding the original by the fabric of the front of his outfit. 

"If we're not the real Legion, just some punks," he said, winding up his free hand like a cartoon character, "Then this will be really embarrassing for you." He swung, socking Multiplus right in the jaw. It was a surprisingly mundane ended to a fight among supers. 

With the original's loss of consciousness, the clones followed suit and started to disappear, freeing up the Legion members that they were fighting. 

Marvel floated down, holding Multiplus in a surprisingly gentle manner, and addressed his comrades. "I'm not really sure what to do with him now, they don't show this part in the comics."