While searching for Tony who was secretly gone in Yamapalu, John Colby distracted Mike by sleeping with him.. Over the next few months he continued to view John as perfect and give Tony all the horrible jobs involving him having to eat something disgusting. While he tried to be more polite, he occasionally lashed out in anger in meetings.
After continually inviting over John over for events like Thanksgiving and being rejected, Applebee returned to his disgruntled ways and would send John and Tony on suicide missions where they'd barely survive. When Applebee sends them on a surveillance mission to review activity at The Church of the Divinity of the Immaculate OVA, he is appalled to hear a mass suicide occurred and blames the two of them for it. He transfers Tony to the Municipal Traffic Division and John to the U.S. Department of Agriculture.
When John sweet-talked his way back into Applebee's bed, Applebee agreed to reinstate them into the U.S. Food and Drug Administration. He was subsequently shocked that John had been sleeping with his USDA boss Director Penya. After brief exchanges of desire for John, they both agreed there was enough of "John" to go around. They both continued to woo John to John's dismay.
After his sister's death, Tony no longer took crap from Applebee. Unable to push Tony around anymore, Applebee found a sounding board in John and cried on his shoulder.
John, Tony and Applebee soon headed to Las Vegas for an FDA conference. When they found beet-flavored vodka at a bar, Tony drank way too much and John drank more to get out of hearing Applebee's stories. However, he soon woke up in the honeymoon suite with Applebee and realized he had just gotten married to Applebee. For the family celebration, John was told he could bring anyone except Tony Chu. As a result, John invited Mason Savoy to the event. He had Applebee and Mason sit down and work out a deal. Mason would help them capture the Vampire Collector in return for them helping him get to the truth of the avian flu.
Caesar, Mason, John, and Poyo soon headed to the Red Bear Bakery where they followed up with one of the Collector's informants. After Olive consumed one of his underlings blood, she knew exactly where to attack the Collector. While they prepared to storm the compound, Tony spoke with John on the phone and told him not to attack. He knew how to take the Collector down per Toni's vision and this was not the way. Applebee ordered them to move forward with the plan anyways. The crew was quickly outmatched by the Collector. The FDA members were saved by NASA and rushed to a nearby hospital.
John visited Mason Savoy in the Our Lady of the Broken Femur Hospital. His husband, Mike Applebee, was about to die. Director Penya stepped in to save Applebee's life for John. She had him reconstructed into a centaur. John was happy and asked if he was anatomically correct. As he was leaving the hospital, Tony asked if he would partner with him once again and take down the Collector. John realized he needed to get Poyo's body out of the dumpster to give Tony his fighting skills. He rushed to the garbage dump but found that Poyo's body had been moved by the garbage man.
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