NOTE: This spoiler was submitted by Jeremy

The film starts with a video documenting the world of Avalonia, a land filled with mystery. Going through this world is the famous explorer Jaeger Clade (Dennis Quaid) and his son Searcher (Jake Gyllenhaal).

Jaeger leads an expedition through a snow-covered part of Avalonia with Searcher and others. At one point, Searcher nearly falls down an icy crevice until Jaeger uses a rope to swing down and rescue his son. As they keep moving forward, Searcher discovers a plant emitting energy. Jaeger is not interested but the rest of the crew is eager to listen to Searcher. Despite pleading with his father, Jaeger just gives Searcher a compass as he heads out alone, disappearing from Searcher’s life.

In the present day, Searcher lives on a farm where he mines Pando, the plant he discovered that is the main energy source for Avalonia. Searcher lives with his pilot wife Meridian (Gabrielle Union) and their son Ethan (Jaboukie Young-White), plus their three-legged dog Legend. Ethan meets with his friends, including his crush Diazo (Jonathan Melo), who come with some trading cards they collect. Diazo gives Ethan a card that he grabbed for him, which touches Ethan. Searcher comes by to embarrass Ethan in front of his friends.

Searcher takes Ethan into the city. While he loves his dad, Ethan doesn’t share the same love for farming that Searcher does. Searcher personally worries that Ethan will grow up to be like Jaeger.

At night, the Clades are visited by Callisto Mal (Lucy Liu), leader of Avalonia and a former crew member of Jaeger’s who knows Searcher as “Baby Clade”. Callisto informs the Clades that there is something wrong with Pando, and that if they don’t solve the problem soon, Avalonia will be in trouble. Searcher joins Callisto but orders Ethan to stay behind for fear of putting him in danger.

Searcher joins Callisto’s ship, the Venture, as they travel down a sinkhole. They then find Meridian riding down in her crop duster, as she informs Searcher that Ethan and Legend stowed away on the ship. Before Searcher can chastise Ethan, the crew is attacked by pink pterodactyl creatures. The ship crashes, and Searcher and Legend are separated from the crew as they crash into a world beneath Avalonia.

Searcher and Legend come across large tentacle monsters called Reapers before they are scared off by a large bearded man with a flamethrower. This turns out to be Jaeger, who doesn’t initially recognize Searcher and believes him to be a hallucination until Searcher gives him back his compass. Searcher is still resentful toward Jaeger for leaving him and his mother, who got remarried. Jaeger admits he felt that he needed to see what was beyond the mountains during his expedition.

While Meridian helps Callisto repair the damage to the ship, Ethan sneaks off and comes across a blue amoeba-like creature called Splat. Ethan takes Splat with him and comes across Pando rocks. When one of them touches Splat, it wounds him. Ethan then tends to the burn on Splat’s body.

Searcher finds a trading card from Ethan’s collection and realizes he’s close. Sure enough, he finds his father and grandfather, meeting Jaeger for the first time after hearing many stories of him. They are attacked by Reapers and the pink bird monsters before they get picked up by Callisto and Meridian and hop back onto the Venture.

Searcher and Jaeger butt heads due to Searcher wanting to finish the mission while Jaeger wants to keep seeing what’s beyond the mountains. Ethan attempts to get them to bond by using his trading cards, but they fail to comprehend it.

The crew passes through green gas clouds before getting attacked by more creatures. They use the Pando rocks to fight them off since it weakens them like it did with Splat. After getting through, Searcher and Jaeger have a heart-to-heart where they appear to reconcile. However, Searcher is still worried about Jaeger’s influence on Ethan since the boy is amazed by the world and might want to become an explorer.

The crew comes across a large mass that is the source of Pando. The Reapers and pink monsters are surrounding it. When Ethan wants to help, he argues with Searcher and attempts to get away from him, but they end up flying past the mountains and finding themselves outside the body of a massive living creature, its eye-opening to see the Clades. They realize that Avalonia IS the creature, and the Pando is killing it since the source mass is surrounding its heart.

Searcher and Ethan return to try and warn everyone, but Jaeger heads off on his own again, and Callisto is set on saving Pando, so she has her crew lock the Clades up. They are freed with help from Legend and Splat.

Searcher and Ethan head to the heart to try and destroy the Pando cluster, while Meridian takes control of the ship from Callisto, allowing her to see the creature’s heart and what is really at stake. The father and son begin to break through the cluster, and are then joined by Jaeger. They break through deep enough for the Reapers to get in and tear up the cluster. After the cluster is destroyed, nothing seems to happen until little orange organisms surround the heart and bring life back to the creature. The crew then flies outside the creature to get a good look at it, with Jaeger now having his goal fulfilled.

One year later, Ethan has decided to stay in the underground world with Splat and Diazo. With Pando gone, Avalonia has moved to wind turbines for energy. Ethan writes to Searcher to let him know he is doing okay. Jaeger goes to visit his ex-wife and meets her new husband. Searcher then does farming with Jaeger, the two of them catching up on many years of bonding.

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The world of Avalonia is mysterious and advanced in technology. Searcher Clade works as a farmer mining the energy source known as Pando, living with his wife Meridian, their son Ethan, and dog Legend. Avalonia’s leader Callisto Mal recruits Searcher for a trip beneath the land to find out what is causing Pando to die out.

The crew is joined by Meridian after Ethan and Legend stow away on Callisto’s ship. Searcher is reunited with his explorer father Jaeger, who disappeared 25 years earlier after venturing on an expedition. Ethan befriends a blue creature that he names Splat. The Clades learn that Avalonia is actually a giant living creature, and the Pando is weakening it. They work together to destroy the cluster and save Avalonia.

Ethan stays in the underground world to explore with Splat and his crush Diazo. Searcher starts to catch up on bonding with Jaeger.