The mangaka took a gamble on a pretty risky premise that seemed to be pointing at a generic harem-romance-comedy-visual novel style story. And boy am I glad this didn't get cancelled/axed early due to skepticism, because the "true story" was set up brilliantly during the early arcs (routes) while hidden in plain sight the entire time.
Here's a breakdown:
Up to chapter 8 we have a generic otaku influenced childhood friend romance story. Though its conclusion was rather abrupt, it sets up a huge plot device what was barely explained but used intensively as sort of a cop-out for the romance to happen.
Chapter 9 we get a first "twist", and for those who didn't read everything in one go (I marathon-ed 1-14) it's a rather hard pill to swallow, and so we see a reviewer below who insist the story ended at ch. 8. Very wrong. Yes, the days repeat, a different girl's route is taken, it's going to be a new romance, but it is at this point where isn't about who the male protagonist going to end up with - kind of story anymore. That plot device mentioned earlier? More pieces of the clues were given so the readers can connect them somewhat.
Chapter 13 we get yet another reset, this time however the protagonist manages to retrieve the "lost" memory he had from his other routes. Armed with this knowledge, the real story starts.
I personally thinks the mangaka could've dragged out a few more "routes" before giving protagonist his collective memories, seeing as this will be the turning point of the story where Link realize he's in a video game and decides to rather than saving Zelda, he's going to break free from the game world (back) into the real world. This is a huge deal and I'm not sure if chapter 13 is too early for this shift.
Revisiting this after 5 years: Rereading it in one sitting allowed me finally understand what happened. Suffice to say the mangaka MUST'VE wanted more time to develop this ending he was going for. Credit to him I can tell this isn't a last minute decision most mangaka do when they've been axed before they even thought about how to end their series. This guy definitely did, just not given enough time.
Summary of what happened during the "confusing part": The two loops that happened earlier (where this manga was looking to be a generic loser romantic comedy), was result of main guy's future self trying to change the past. Why? Because in both loops we saw during this time in his high school his sister ended up going to America and gets absorbed by a super computer to become a sentient computer developed by his dad who died prior to finishing it. Obviously the high school version won't figure this out until much later and vowed to prevent it. The two loops was him failing to change anything, but helped two versions of his HS self getting laid.
The third loop to my understanding (and this is where the mangaka ran out of pages to explain this shit), he decided to send the sentient-computer that absorbed his sister years ago back somehow. This allowed the HS version to find out the truth and can thus can properly come up with a way to prevent sister from leaving (here's a rushed sideplot where the sentient-computer don't want help because if she succeeds then she wouldn't exist anymore because of paradox and she's in love with our main guy apparently). And to get best of both worlds HS guy says he'll find a way to save his sister as well as the sentient-computer from the future which only exist because it absorbed his sister.
More rushed nonsense, the solution turned out to be our guy chose to get absorbed himself instead of the sister. Resulting in an immediate future where his future sister is trying to figure out how to save her brother from being absorbed in a reverse role situation. Then even MORE rush happens we're led to the ending where everything worked out. Future sister appeared into Future main guy's time line and they reunite and hug. And HS main guy and his sister grows closer (despite they have no memory of the tragedy that was prevented.)
All in all it's a shame this didn't get more chapters. Consider we have generic trash like Nisekoi getting like 20 volumes.