20th Century Boys/WMG

Friend is Light Yagami.
It turns out that the virus he has created is only a bluff and that the Book of Prophecy is just only a Death Note in disguised.

Friend is The Joker.
The laughing gas is the virus that Friend plans to unleash to the world.

Friend was trying to protect the Earth from a real alien invasion
He was only evil because there was a bigger threat on the horizon, like Scorpius, or one of those other Well Intentioned Extremists.

Friend is Alex Mercer
.

Friend is Taro Mitsuki.
If you think he is going to Germany, think again. He is leaving to Japan and plans on causing destruction as a masked villain. Why? He lost Sara to Gackto.

Friend is Johan Liebert.
After leaving the hospital, Johan figures he'll go start up some shit in Tenma's home country, Japan. There he meets, from whom he takes the "Book of Prophesy" from and decides to start up the Cult of Friendship. When the going got tough, Johan picked to be the scapegoat. In addition, is not Kanna's father — Johan is, which also explains why Kanna shares a physical resemblance to Johan's sister, Anna, and is apparently the only Urasawa character to be affected by Mukokuseki.

Friend is actually working for Asbergo Industries.
Given their goal, his working for them would make perfect sense.