That’s how he was shoved into that Wonderball, never to return to the real world.

One of the trenches held the strange ball in front of him.
“What is this?” asked Ed in a disgusted tone.
“This” said the trench, “is your new home.”

Ed recognized the voice from somewhere, but couldn’t put his finger on it. Suddenly it hit him.
“Chris…?”
The trench smiled.
“Yes, Ed…”
“But… why? After all we’ve been through, after all we fought? You’re giving up…”
Chris shook his head.
“This is for your own good, Ed. And besides, i haven’t given up. This is only the beginning. You will see the glorious light of day again, my friend. But for now they must believe that you have been finished off.”
He cracked open the wonderball, which swirled with seemingly tangible blue and gold light. He took Ed by his shirt.
“I’m sorry, brother… I promise you I’ll come back. Don’t ever doubt my words, Ed. I will come back.”

With that, he shoved Ed into the Wonderball, the tangible light disappearing.