I'm glad they are going for the predictable "twist" that follow their build up for the plot points that really matter. Makoto's dream that Yukiko was missing was in fact a memory from his past life, all his day dreams that hinted at the fake city were. What's interesting is that there are three characters who know about Shinjuku, the second one is Yukiko who like Makoto saw it in her dreams (and like original Makoto lives in the real Shinjuku) and the third one is Ai, who before dying in the first chapter says "You finally remembered! Please take me with you to shinjuku". The original Ai lives in the virtual world with her memories intact for decades now incapable of escaping since she is dead, and seems to be aware that Makoto is from the other side.
The creation of a "world where Ai doesn't die" was already mentioned before, in the Patissier's world (who looked like Ai possibly because she was herself an experiment based on Ai's memory to create said world, and we know there are other copies of her around). In the Patissier's world the setting is similar to the real world, we see that Ai can't pay for college so it's likely that she couldn't pay either for the medical costs of keeping her alive, so Makoto had to work to pay for it by getting the funds from his research in AI and virtual reality (which allegedly escalated into the end of the world). And Ai herself denies that world, since that's Makoto's (dream) world, not their (the real) world. The real Makoto she loves is still outside, dying alone after spending all of his lifespan working for someone who was already dead .
There is still a lot of things to be explained though, in particular who really is Yukiko? What exactly prevents real Makoto to upload Ai's mind to Inaba's body like he did with Makoto? Why Ai dies whenever she is confessed to (and why she only stops pretending to not remember during these times)? And obviously the entire real world situation, but after this chapter I don't think it will be an important plot point.