After the events of Neo-Tokyo being wiped out, the US military arrived to collect the survivors. The General is now stripped of his rank and is now a soldier in the US military. Kei, Kai, and Kaneda were arrested for questioning regarding the explosion. 24 years later, Kaneda is now in his late 30's, and Kei and Kai in their 40's. They were released from prison on parole. The year, was now 2043, a time of great innovation, and technological advancement. Corporations have more power than the government, and civil unrest was high. After the fall of Neo-Tokyo, other cities were afraid of suffering the same fate.
Kaneda during his years is now wiser and depressed, knowing that Tetsuo was right; he did order Tetsuo around too much, and he was too arrogant to see that he was also in the wrong. He deeply regretted his attempts to kill him, but knew that he had to in order to save the people of Neo-Tokyo. Tetsuo's death stood as his greatest failure. He was massively suicidal, but his two friends were there to remind them that he has to live for those he cares about, no matter what life throws at him. He and Kei are now in a relationship. Kai is a friend, and the General has now joined the team, realizing that they may be the only hope for a brighter future.
Because of the explosion, fallout from Tetsuo and Akira's bomb spread across Neo-Tokyo, killing thousands. There were a number of survivors, but the most well-known are the General, Kaneda, Kei, and Kai. However, the other survivors were infected with the fallout, and begin to develop psychic powers similar to Tetsuo. They plan to take over the world, and annihilate most of humanity, seeing themselves as the superior race.
Whew, that's what I've come up with, but it'll be nowhere near as close to what Katsuhiro Otomo would come up. Just an idea.