Here is my theory for the missing parts of this work.
I think everything can be explained if we consider HADES a clone of Akira. And that all the survivors of the disaster are also clones.
In the story of Akira's mother we have two important clues, first of all in the conversation with her secretary we understand that the initial project has been modified, the secretary is too worried by these changes to refer only to the fourth tower. Akira's mother probably changed something else too.
The second clue is Akira's mother's dream. It certainly can be explained as a premonitory dream full of hope, but what if it was a representation of what she was working on? That is, an island on which to bring her son and her friends back to life, in the form of clones.
It may seem absurd, but on Raika Island, they are able to bring back life forms that existed millions of years before, is it really so absurd that they can clone human beings?
Returning to the present, or rather the future, we have other clues on the island
1) The school, why recreate a building perfectly identical to the original, if not to make it easier for the kids to settle in?
2) Then we have the same name as the island, RAIKA ISLAND, where raika is the anagram of akira, and therefore we could read it as Akira's island. Another clue that Akira's mother diverted the project from origins (Why would Mina's grandfather use Akira's anagram?)
3) The fact that Akira wakes up after the accident far from the others, perhaps because the Akira who woke up on the island is not the one on the plane.
4) Under the pyramid we have the laboratory where the monsters are created, but are we sure there isn't anything else? The incubators we see broken may in fact be meant not for creatures, but for humans
Another interesting point is the model of the island, which inspires me. Don't you find it strange that there was also a model of the plane? I believe they were recreating the entire incident on the island. But we'll talk about it later.
Now back to HADES and the fact that he is Akira's clone. In my opinion it may not be a simple clone, but a failed prototype of cloning, the mask could hide a disfigured face, or he is simply wearing it to hide his appearance. His build and hair are similar to Akira's, he wears a uniform and in the end we discover that he has formed a relationship with Kouehi, who trusts him without too many problems. We also never see Hades hurt the kids, even kouehi's actions can't be blamed on him. Hades lets Kouehi know that he knows who killed the pilot, but Kouehi is the one who carried out the massacre.
So in my opinion Hades is a corrupted version of akira and it could have been him who destroyed the island, he could in fact have poisoned the staff in the school and then caused the accidents in the other towers with the aim of eliminating everyone who lived there. The reason? I honestly couldn't justify this except with the fact that as a corrupt clone he may have developed mental damage.
PS: We can give a possible motivation for Hades' actions if we take into consideration the model of the plane mentioned previously, but his explanation may be even crazier than what has been said so far. In fact, we can hypothesize that the entire project involved recreating the plane crash so that Akira and the others, or rather their clones, could experience the adventure that Akira's mother had dreamed of, obviously in a controlled environment, but the actions of hades instead meant that the situation was very different from what had been prepared. This is because Hades may have developed a corrupt sense of justice, and therefore tried to stop the project before it started, because what is dead must stay dead.
PSS: Of course the manga was closed very quickly, hastily, this would justify the holes that these theories have.