After the cinematics, you will play as the Gaia Colossus dashing through Dark Gaia with the correct button. Dodge or smash the rocks to reach Dark Gaia and get closer. He will shoot a laser after awhile. When he is about to shoot, guard and move to a side to dodge it. You will get hit at least two times. You will then go into a "quick thinking" phase were you have to press the correct buttons. If done correctly, Dark Gaia will get a hold of you and you will play as Sonic. As you go through the Colossus, you will have to press the correct buttons to hit Dark Gaia's big eyes. You will have to repeat this all two more times, then stage gets harder. After you are done, you will enter the Super Sonic stage, where you will start to fly towards Perfect Dark Gaia. When you get near the Force Shield, Chip will enter the shield in the Colossus. You will then have to hit the snakes outside of the shield as their heads leave it. As you hit the snakes, Dark Gaia will attack. Avoid the rocks and lasers he shoots. After you knock out all the snakes, the shield will drop. Then Dark Gaia will grab the Gaia Colossus. You will now have to press the correct buttons to save him using Super Sonic. After you free the Gaia Colossus, Dark Gaia will shoot a laser at it. You will have to press a particular button a certain number of times to block it. If done correctly, Super Sonic will fly towards Dark Gaia's middle eye. You can use [Boost] while flying there if desired. When it is over, your grade will be based on how fast you did it.
Defeat the final Boss and successfully complete the game.
Complete each condition to get the allotted Trophies. There are 35 Bronze Trophies, 14 Silver Trophies, 1 Gold Trophy, and 1 Platinum Trophy.
Trophy | How to unlock
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| - This is the platinum trophy and is unlocked automatically when all the trophies have been unlocked
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| - Cleared Act 1 of Tornado Defense without taking damage
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| - Have mastered the Air Boost technique
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| - Restored the fifth continent
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| - Have attained Combat Level 5
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| - Became best friends with Chip.
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| - Reached the Goal of Windmill Isle, Act 2 as Sonic within 2'35"
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| - Upgraded all of Sonic the Hedgehog's stats to their maximum levels
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| - Achieved 10,000 total combos
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| - Have attained Combat Level 15
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- Creature of the Night (Bronze)
| - Achieved an S Rank with Sonic the Werehog for the first time
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| - Cleared all Sonic the Hedgehog stages
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| - Cleared all hot dog stand missions in Mazuri
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- First Time Customer (Bronze)
| - Bought a product from Wentos
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| - Cleared all hot dog stand missions in Adabat
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| - Collected all Moon Medals
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- Get on the Exorcise Bandwagon (Bronze)
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- Getting the Hang of Things (Bronze)
| - Achieved an S Rank with Sonic the Hedgehog for the first time
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- Gyro with Relish (Bronze)
| - Cleared all hot dog stand missions in Apotos
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| - Collected half of the Moon Medals
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| - Cleared all hot dog stand missions in Eggmanland
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- Hard Day's Night (Bronze)
| - Cleared all Sonic the Werehog stages
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| - Cleared the Louie Montaine missions in Empire City and the Ana missions in Mazuri
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| - Completed all missions for a townsperson
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- Hungry Hungry Hedgehog (Silver)
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| - Have mastered the Lightspeed Dash technique
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- I Ain't Afraid of No Ghost (Bronze)
| - Cleared the Marcantonio missions in Spagonia
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| - Cleared all hot dog stand missions in Holoska
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| - Cleared all hot dog stand missions in Shamar
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- Ketchup and Mustard (Bronze)
| - Cleared all hot dog stand missions in Empire City
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- Knockout Brawler (Silver)
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- Lay the Smackdown (Bronze)
| - Have mastered the Stomp technique
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| - Restored the second continent
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- Oh, You Shouldn't Have! (Bronze)
| - Gave a souvenir to the Professor
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| - Restored the sixth continent
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| - Collected half of the Sun Medals
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- Picking Up the Pieces (Bronze)
| - Restored the fourth continent
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- Pig in a Blanket (Bronze)
| - Cleared all hot dog stand missions in Spagonia
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- Power Overwhelming (Silver)
| - Upgraded all of Sonic the Werehog's stats to their maximum levels
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| - Collected 5,000 total rings
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- Sausage Fried Rice (Bronze)
| - Cleared all hot dog stand missions in Chun-nan
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| - Have attained Combat Level 10
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- Social Butterfly (Silver)
| - Talked to all townspeople
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| - Reached the Goal of Arid Sands, Act 1 as Sonic within 2'50"
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- Still a Jigsaw Puzzle (Bronze)
| - Restored the third continent
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| - Restored the first continent
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- That's Enough, Seriously (Bronze)
| - Gave all souvenirs to the Professor
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| - Have attained Combat Level 20
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| - Have mastered the Wall Jump technique
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