There are a lot of mysteries on the island. Akira's Group encounter them on a daily basis. Some mysteries are easy to resolve. Other mysteries are are yet unknown.
A major mystery of the island is where and what is it. This is encountered at the very start of the island considering the fact that it isn't on any maps. Next would be why are there extinct animals on the island? There are a variety of extinct animals that have appeared throughout the series that should have lived in different timelines entirely and completely different countries.
Despite fruit being a major trial to overcome whilst surviving at an unknown area, on the island there is a huge amount of fruit and food for humans and other animals to consume. Why there is so many is unknown, Shirou Mariya adresses this problem in chapter 53.
The timeline of the island is also unknown. Considering that there are monuments like the pyramid and obelisk that seem like they come from the past, there is also the lighthouse building which has high tech computers in it.
On Chapter 3, there is a page filled with previews what is yet to come. Some has yet to revealed.
At the end of each arcs there are some question left unanswered. The readers want to know about it like:
- Wonderful World arc
- Why are some passengers wake up in the middle of the jungle (Akira Sengoku, Shirou Mariya and Kanako Oomori) or the rocky cliff east of the plane(Rei Ooguro, Kotomi Kawana and Tooru Rinzai). While most passengers wake up inside the plane?
- When Akira, Shirou and Kanako found the pilot the knife is still stabbed at his chest. Later on Kouhei use a knife to stab Kanako. Is it the same knife?
- The same goes to Makoto's camera. He left it on the plane for Akira's Group to find it. Later on Makoto use another camera to film on top of Cursed Mountain. Does he have enough batteries for it?
- Who is Hades? A old friend of Akira?
- Raft arc
- How big is the 'Ocean' lake? Can it lead to the real ocean?
- Epidemic arc
- The side story with Kouhei's Group. Hades manages to track Kouhei's Group since they are at least 1 day distance from the plane. Does he also have a vendette against Kouhei?
- When Akira's Group found the pilot the knife is still stabbed at his chest. They buried the pilot. The knife is never mentioned again. Later on Hades threw a knife toward Kouhei. Is it the same knife?
- Adult Camp arc
- Brain Loss arc
- Did Kouhei really die when the waterflood hit him?
- Kouhei survives and was pulled out of the river by Hades. He returns in Chapter 150 and leaves at the end of the story arc.
- School arc
- What is the name of the school that Akira and fellow students go to?
- They go to Meikyou Middle School.
- Exploration Party arc
- How many more university students are on the plane aside from Kawana Kotomi, Rei Ooguro and Tooru Rinzai?
- Argentavis arc
- Cursed Mountain arc
- How many group have successful crossed over the mountain aside from Akira's Group, Makoto's Group, and Kouichi's Group?
- What happened to the rest of the group of Nagatsuka, and Noriaki Matsuki? Did they die on the mountain?
- Mami the Clairvoyant arc
- Gigantopithecus arc
- Is Makoto Morita the original creator of building rock towers? Did someone else build it first?
- Did Kazuma Saji really die when he falls from a cliff down into a current river?
- After they fleed the forest and they decided to rest by the river why did Miina Isurugi (Fake) get to bath with the rest of the ladies. Didn't he have a 'hard' incident while riding behind Rei at the 'Cursed Mountain'
- Are Momoka Kirino and Touko used to be apart of the same group as Matsuki and Nagatsuka. Akira's Group encounter the duos just after they enter Cursed Mountain and Huge Jungle?
- Obelisk arc
- Who built/first discover The Tower and what is its function? Answer Chapter 100 (maybe)
- What is the meaning of the statue?
- Kouichi’s side story. Who built the raft by the ocean? Since Kazuma's raft lies at the shoreline by the lake.
- Is the mountain really man-made?
- Animal Battle arc
- Pyramid arc
- Failed Experiment arc
- Showdown arc
- Operation arc
- Tower of Death arc