This ending is kind of poopy. The ending theory I came out with 5 months ago was better:
My theory on what is going on after the events of the last few chapters including chapter 33, including some theorizing on the future:
So every human on earth was put in a dream state by a A.I. The A.I could simulate everything in these dream worlds, memories, money, traveling, people, except love. So most humans killed themselves like Makoto was about to do in the fake world the patisserie created for him. Also, perhaps the A.I. went rogue and starting turning everyone who doubted the world into puppets. Only 2 humans are still alive and "thinking".
So Ai is probably an A.I as well, since she got ripped apart too, and is based off the real Ai who is either sick or dead in the real world. Maybe real Ai's brain/memories were digitized and put in the fake world. Ruka is likely an A.I, he has likely has fake memories of his mother. He has also shown exceptional cruelty by having Ai confess 564 times. Also, notice how Ruka was perfectly content letting that one puppet shoot Yukiko, until makoto sacrificed himself for Yukiko, he did not understand what sacrifice was. He doesn't know he is an Ai though. Makoto is probably real, probably had his memories of the real world blocked off. He had to leave Ai, since she was sick, while he went to shinjuki station to help old man. She wanted to go with Makoto, but she couldn't. But Makoto put her in the fake world before he left. Since Makoto and Yukiko are the only ones who have expressed love (for Ai), they are both real. i.e. the last two humans "thinking".
The fake-yukiko that is helping the old man is just an android modeled after the real yukiko. Real yukiko is someone related to old man, maybe a granddaughter or something. Old man doesn't want the android's help fixing humanity's problems, becaues that was what caused the apocalypse in the first place. Old man put Makoto and Yukiko in an isolated test environment, the city of imprisoned love. There might be others that were also put in isolated test environments, but they all failed. This is why they can't leave, because old man needs them to stay in the city for the test to save humanity.
Old man is trying to see if either the A.I., or Ai, or Ruka, can be taught to understand love. Because then maybe humanity can be saved. The 3 keys enable either makoto or yukiko to leave the city, but only 1 can leave. They will have to decide between each other who loves Ai more (or who does Ai love more) and deserve to leave more. Maybe they will both decide to decide stay in the city with Ai, and let Ruka leave. They will realize Ai is dead on the outside, or there is no saving her. And there is no saving humanity either, that ship has sailed.
Since Ruka is not real, he has no actual body to go to. Yukiko android will offer to let old man transfer Ruka's conciousness to herself. Yukiko android does not really care about living or dieing, it's just an android that exists to help the old man. It is at this moment that the A.I will understand love, by them offering to let Ruka, an A.I leave. Also, by both Makoto and Yukiko not willing to leave each other alone in city. These acts of selflessness will make the A.I understand the wrongs that it has done. Make it understand that humans need love. They will both be able to confess to Ai after this. By transfering Ruka's conciousness to Yukiko android, he will have created the first fully artificial human, capable of feeling all the emotions of actual humans, and start a new type of civiliation. Ruka is very smart and scientifically minded, and can continue the old man's work in scientific stuff. Before old man dies, he will open up the fake world to Makoto, Yukiko, and Ai, and allow them to leave the city (but still be in the fake world) and live their lives together. Android Yukiko/Ruka will simultaneously be both modern day Adam and Eve, being a male A.I. in a female android's body.