However, Knuckles crashed their shuttle on the Space Colony ARK, and Amy was enraged by Sonic and Tails leaving her behind. They showed Tails and Sonic and they managed to defeat the Egg Golem and make their way into space. She then saw Eggman go into a pyramid with Rouge.
She then angrily watched as Tails left her and Knuckles behind as he raced in the Cyclone down Route 101. She then puzzled at the thought of Eggman taking the six Chaos Emeralds into outer space, when Knuckles emerged from the Aquatic Mine. They then fled the police, when Amy realized they were after her too, so she ran after Tails. Suddenly, Amy noticed that half of the moon was gone due to Eggman destroying it with the Eclipse Cannon. Tails then saved her in the Cyclone, before leaving her to rescue Sonic on his own, but Amy continued to free Sonic and escaped the island with him and Tails. She fled, only to be cornered by Eggman's Egg Walker. However, when he got there, she found him and hugged him when she realized this was actually a black hedgehog working with Eggman. Horrified by this and seeing a chance to get Sonic to notice her, Amy snuck aboard the Tornado 3 and Tails unintentionally brought her with him to Prison Island. for stealing a Chaos Emerald and put in prison on Prison Island.
She also became friends with Miles 'Tails' Prower and Knuckles the Echidna and enemies with Dr. Amy suddenly met Sonic the Hedgehog and developed a crush on him.
