Captain Whisker was tasked by Eggman Nega and Dr. Eggman with capturing the Jeweled Scepter, but in his quest came head-to-head with Blaze the Cat and Sonic the Hedgehog. After a number of clashes, he was defeated, despite being joined in battle by his first mate Johnny. (SRA)
Scourge of the Sol Zone
Still answering to Nega, Whisker and his crew were forced to contend with a new rival on the Sol Zone seas: Captain Metal in his Metal Marauder. Johnny managed to score a victory by stealing a Sol Emerald from Bark the Polar Bear and Bean the Dynamite, who had recently stolen it from Metal himself. However, the theft brought Whisker under attack not only from Metal's forces but also the members of Team Rose. Both Whisker's vessel and the Marauder were subsequently attacked by Metal's Kraken, and the explosion that destroyed it also sent the Emerald flying back into Metal's clutches. The battle between vessels continued briefly, until Whisker realized that Metal intended to power up his Egg O' War using the Sol Emeralds. He thus beat a hasty retreat, and was joined by the Marauder's crew after blowing a hole through the ship that led to it's sinking. (SU: #57, #58)
Captain Whisker is a cruel robot with a hot temper often aggravated by his subordinates, especially Mini and Mum. While he serves Eggman Nega, Whisker apparently rebels at the notion of obedience to the doctor-not unlike the Pre-Super Genesis Wave Timeline Prime Zone's Crocbot-and anticipates the day when he will be able to rebel against his master.
- The fact that Blaze thought Whisker might still be a threat to her people in SU #1 indicates that he survived his defeat in Sonic Rush Adventure Writer Ian Flynn has also said that he doesn't "recall it being implied he was destroyed at the end of Sonic Rush Adventure, so I'm assuming he's still active."  This would later be confirmed in SU #57.