Yogi leads his friends on a tour of the "Spruce Goose", the world-famous flying boat / aircraft, built by billionaire Howard Hughes. While touring, they were accidentally locked inside the plane. To make matters more worse, the dome where the plane was located closed up for the night. As the gang tried to get out, Augie Doggie tripped over and opened a door. Now the gang walked down a corridor and soon they came to the cockpit. While looking for a button or switch to open a door, Yogi pushed a button which magically activated the plane. Soon the gang exited the dome in the plane. In an attempt to avoid a bridge, Yogi pulls back the wheel, causing the Spruce Goose to lift off. The plane nearly collides with the RMS Queen Mary Hotel, but is able to lift off and avoid the ship. A segment then occurs where the Spruce Goose is in outer space, and the gang begins seeing images of each other drawn in the stars. Later we see two aliens, Merkin and Firkin, trying to invade earth by posing as "Earth people", but they were scared away from California by the Spruce Goose.
Next, Yogi and his friends listen to the radio about a group of arctic animals down at the South Pole trapped by a snowstorm and unable to reach the open sea. So they fly down there to help. While flying over to the spot where the animals are trapped, they stopped to help an injured pelican. Then they met a young girl with an attitude named Bernice, who had been on the Spruce Goose tour with her mom before getting lost herself. Soon they arrive to save the animals. They did that by having the Spruce Goose plow through the ice like a giant icebreaker and open a channel to the ocean. They succeeded, but their mission wasn't finished yet, as the penguins were attacked by sharks. So they got the plane to act as a bridge to get the penguins safely across the water. Suddenly, Bernice tripped a fell onto a propeller. Yogi saved her, but he wound up hanging onto the propeller instead. Quick Draw McGraw arrived to save Yogi, but soon all three of them fell off the plane and landed on an ice pack due to Snagglepuss' attempt to swing Yogi back up via starting the engines. The sharks approached the three gang members in peril, but they were scared off by a whale who saved the group. The whale took them back to the Spruce Goose and the gang then flew away.
Next, Yogi and his friends listen to the radio about a bunch of animals trapped on an ocean liner at the Zelman Sea, long after poachers kidnapped them and left them on the boat to die. Though they had a hard time finding the Zelman Sea, they eventually found the sea and started off towards the ocean liner. Merkin and Firkin later showed up again and located the unmanned ocean liner full of abandoned poached animals and decide to start their invasion there. They transform into "Earth animals" in an attempt to, once again, mingle among them. All of a sudden, once again, they are scared by the oncoming Spruce Goose and leave again. The gang arrives to save the animals. At first they tried to tow the ship by tying the ropes to the doors at the bow of the ship, but the doors eventually opened up and caused the water to enter the ship, threatening to sink it and drown the animals. Quick Draw McGraw as El Kabong tried to rescue the animals himself but with little success. Then Bernice found a way to save the animals; it was to open the cargo doors upfront and bring them on board. At first they couldn't find the doors since the nose of the plane was altered after its only flight years ago. But after a round of clapping, the doors were finally located and opened up for the animals to enter the Spruce Goose. The gang then flew the animals to the nearest island with the word "HELP" written on the sand (Yogi thought this was the island's name) and released the animals.
After rescuing the animals, Boo Boo told Yogi that there's no such island called "Help" and realizes that somebody else is on the island and wrote the word down into the sand to call for help. So the gang starts a search party, but unbeknownst to them something is lurking in the bushes listening in on them. The thing in the bushes is revealed to be Mumbly, who has crashed on the island along with the Dread Baron. Mumbly then awakens The Dread Baron and attempts to tell him of the plane. Looking through a telescope, The Dread Baron realizes the plane is the Spruce Goose, and that with it he can become rich. He then notices Yogi and his gang and realizes his plans could be foiled by them. But after seeing Bernice with the gang, he devises a plan to get on the Spruce Goose and try to take it over. When Bernice goes off looking by herself, she becomes stuck in quicksand. The Dread Baron attempts to save her, but he is stuck himself while Bernice emerges. Then a yell out of help brought the gang to his attention. When they first encountered him, the entire group voted as to whether or not the Dread Baron and Mumbly can come with Yogi's gang. The gang (except Yogi) resisted, Yogi calling it a mutiny, but then a pelican (different from the one from earlier) flew to her nest. But one of her eggs fell out and Bernice catches it. Yogi decided to make Dread Baron take it back to the nest as a way testing him to see if he's reformed or not (which of course he isn't). After an argument with Mumbly, they eventually went on their way and after climbing up mountains and facing killer animals, they brought it back to the nest. Before they left the nest however, the eggs hatched and the birds that came out of them quickly realized that they were looking at the Dread Baron. So they peck him good and Mumbly naturally enjoyed it. Finally, Yogi allowed the wicked flyers on the plane and the Dread Baron started to plot on how to takeover the Spruce Goose.
On the Spruce Goose while Yogi and Boo Boo sing "Back to the USA", DB and Mumbly did some clean up work so that they won't raise any suspicions (they drowned out the song while they were doing it). Yogi checked up on them and find that they were doing a great job. Then DB throws a party for the gang supposedly as a matter of thanks. But the party was a trap as DB traps them in a cargo hold where the party was held. So now Dread Baron takes over the plane and he and Mumbly flew off to where they were supposed to go a long time ago (before they crashed). It was to the Island of Moolah Moolah.
They reached the island by accidentally landing on its volcano. Then after a good night's sleep, they set afoot on the island. The island is filled with natives who worship an idol that looks like Dread Baron. They called it, "Malagula." Dread Baron posing as Malagula parachuted down to the ground and surprised the natives. At first, the natives gave him vases, but he didn't want them. Malagula wanted gold, so they gave lots of it to him. Meanwhile, the gang still locked in the cargo hold found a way to get out by tricking the native guarding the door. The native chased the gang but they exited the plane by crazily riding a palm tree. The gang confronted Dread Baron but he ultimately captured them and sent them to a hut to imprison them. But with quick thinking, the gang took the hut and started to run. As they ran, they approached a hole. Supposedly, they wanted to jump into the hole and climb out, but the hole was filled with crocodiles and they bit and scared the gang out. Malagula and the natives surrounded the gang after they landed on the ground and were about to decide what to do with the gang next when the volcano started to erupt. With the natives and Malagula in shock, the gang escaped back to the plane. As they escaped, the volcano caused a fault to crack and destroy the Malagula idol. This caused the natives to believe the volcano was mad at Malagula and stop worshiping him and chased Dread Baron and Mumbly back to the plane. After that we get one last look at Merkin and Firkin who flew to Moolah Moolah, thinking that they finally found a spot to invade Earth in safety. Meanwhile, the Spruce Goose was struggling to take off. Dread Baron angrily said that plane can't take off from a mountaintop and needed room to taxi. Boo Boo fears that they're now doomed and it looks as if Merkin and Firkin have it made. But gigantic pressures cause the plane to go back in the air and scare off Merkin and Firkin one last time. But the plane wasn't out of danger yet; for the weight of all the gold that's in there started to bring it down and stall the engines. So the gang pushed and shoved the gold out of the plane. Naturally, Dread Baron disapproves and he and Mumbly jumped out to get it. DB tried to parachute down, but the parachute was taken by Mumbly. Somehow they swam back to Moolah Moolah, but with Mumbly as the new idol/island leader and Dread Baron as a slave native, much to his chagrin.
Now with all the gold out of the plane, the gang flew back to Long Beach, California, USA and the dome home of the Spruce Goose. They then went to sleep, but hours later they wake up by the locked door which by that point was opened by an angry janitor. The next day, the gang hopped on their tour bus, said goodbye to Bernice, and went home. Driving home, they hear the stories on the radio of how animals were saved at the South Pole and at the Zelman Sea, to which he claims nobody knows how it happened. Yogi claims he knows how it all happened as he and the gang cheer for the Spruce Goose.
On July 28, 1988, the movie was released on VHS in the United States by Worldvision Home Video. However, as of 2009, the videocassette is now out of print. On December 7, 2010, Warner Archive released Yogi Bear and the Magical Flight of Spruce Goose on DVD in NTSC picture format with all region encoding. This is a Manufacture-on-Demand (MOD) release, available exclusively through Warner's online store and Amazon.com.
On the end credits of the movie it was stated that "The Spruce Goose is located in Long Beach California". In 1992 the Spruce Goose was moved from Long Beach to the Evergreen Aviation & Space Museum located in McMinnville, Oregon, where it resides today.
Yogi and the Invasion of the Space Bears was released in 1988.