The Formation of Agents of Atlas
Khanata is placed as the head of the investigation of Jimmy Woo who, on his last mission for S.H.I.E.L.D, went rogue, leading a team of agents into the San Francisco branch of The Atlas Foundation. Inside the facility, they find a secret room and the team is all killed except for Woo. He is found by S.H.I.E.L.D. and taken back to a S.H.I.E.L.D. facility with very little brain function and on life support. Dugan brought in Gorilla Man for questioning as the only clues they had linked this mission to the original G-Men and Hale was the only member they could contact. With no knowledge of what Woo had done, Hale requested to say a final goodbye, but Hale instead contacted M-11 and Marvel Boy who rescue him while Khanata watches, unable to stop the escape.
Suspecting Marvel Boy's involvement Khanata contacts Mister Fantastic for conformation.Reed however tells Khanata that it's not possible for it to be Marvel Boy due to his death during there encounter. (Unknown to Reed the Marvel Boy they encountered was in fact Thelius, a duplicate of the original Marvel Boy. After ending the call with Reed he informed Dum Dum Dugan that his cousin had discovered the origin of the Gorilla Man in Africa and Dugan informed Khanata that he had gained a promotion into Woo's job. Khanata traveled to Woo's house for clues and find's the G-Men already there, not only learning of Woo's regained youth but also his lack of memories. The G-Men attempted to leave without Khanata but he reveals he has discovered the whereabouts of Venus. Travelling with the group to Africa, the G-Men met Khanata's cousin, who found Venus at the site of Gorilla Man's transformation, having turned the war torn area peaceful. But soon after their arrival Yellow Claw attacked the group.
After a small scuffle Yellow Claw was revealed to have been a robot and Jimmy was rescued by his team-mates. Leaving Africa with Venus, the team return to where Jimmy was initially injured in hopes of finding a temple, however they find nothing. Leaving M-11 behind, Woo and team travel to an old coffee shop Woo used to visit, Gorilla Man reveals M-11 visited him before SHIELD did to inform Hale that he needed to rescue Woo and Marvel Boy revealed his origins and how there was a second version of himself. As the story concludes, the team sees M-11 trying to travel to Anatartica since he has concluded that Namora isn't dead and needs to be rescued. Travelling there they find what appears to be the remains of Namora. 
Namora was revealed to be alive by Marvel Boy and while M-11 freed Namora, the rest of the team were attacked by giant crabs and were rescued by a newly revived Namora. Feeling that he has taken his team aware from there lives, Jimmy tries to send the rest of the team home but they all refused and plan to continue helping him investigating. Using a list complied by Woo before he lost his memories, they began to investigate all possible operations of the Atlas Foundation, with every single site they visit being one. After taking down some pirates, the team is attacked again by Yellow Claw and his terracota army, in the fight Yellow Claw escaped and not even Grayson could detect his presence. After the attack Jimmy confided in Khanata that he suspected on his team to be a traitor
During the search, Namora revealed the secret about Venus' true nature, having known of the legend of the Siren. Venus fell into depression and filled all of her companions with despair. This caused Marvel Boy to reveal the fact that Jimmy suspected M-11 of being the traitor in the midst. While the rest of the team began to fight each other, Woo calmed her and was able to help her rediscover her confidence. Venus proceeded to sing, soothing the rest of the team and they returned to their mission to take down the Atlas group. 
Woo and his team go back to the San Francisco branch of Atlas and re-enter the hidden room. This time, they survive and confront Yellow Claw and Mr. Lao. It turns out that Yellow Claw was waiting for Woo to come, to claim the mantle of Gengis Khan. With the title of Great Khan, Woo also assumed control over the holdings of The Atlas Foundation. Jimmy then asked Khanata to lie to S.H.I.E.L.D. and tell them that they actually perished in the temple so they can continue in secret.
- 30 Appearances of Derek Khanata (Earth-616)
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