Apparently, Bob and A.I.M. did part ways, as he refocused his energy on creating the world's largest popcorn kernel. He funded this project with the money Deadpool had left him with when stranded on that island, but it was all for nothing when Deadpool crashed into the kernel on his way back from outer space. The kernel exploded into a giant piece of popcorn, and then the needy Deadpool tried to ascertain from Bob if he and all of Wade's other friends actually loved him. Bob admitted that he was mostly terrified of Wade and that all of his friends mostly hated him.
In fact, all of Deadpool's friends were being led by a man named Macho Gomez in an effort to kill Wade. After Bob explained how actions like stranding him on an island and destroying his life's work of a giant popcorn kernel made him a bad friend, Wade worked out that Bob had texted Macho Gomez that Wade was at his house. Wade promised Bob he would kill him last. After a bloody battle in which Wade incapacitated or killed a majority of his former allies, Wade realized that the reason he treated his friends so badly. Wade wanted to die and only someone that truly cared about him would kill him like he wanted. After hearing this, Bob assured Wade that he cared and Wade responded by shooting him in the leg again. [Deadpool (3rd series) #36]
Wade next enlisted Bob's help when someone was trying to kill him using a serum that, if injected into Wade, would remove his healing factor. Bob was peeved that Wade had shot him the last time they were together and didn't want to help. So, of course, Wade shot Bob again in order to help convince him to change his mind. This did push Bob into action, but to betray Wade instead. He went to the Kingpin, asking him to procure the serum so Bob could kill Wade himself. Kingpin didn't buy Bob's act, as he stated that anyone that Deadpool had shot multiple times without killing must actually be his friend. Bob admitted that what he really wanted was to make Wade killable in order to instill some empathy in him. Kingpin refused to help Bob and forcefully threw him out of his office, but he did order his assassin Typhoid Mary to retrieve the serum.
After telling Kingpin about the serum, Bob was apparently still working with Deadpool, who gave 
him a mission. Bob next talked to Tombstone about helping him take down Wade, but he was no more receptive than Kingpin about working with the weak Hydra agent. Instead, Tombstone went and told Kingpin about the plan and Typhoid Mary kidnapped Bob to use as bait for Deadpool. Wade found Bob but told him he had more important things to do than rescue him at the moment, though he admitted it was mostly because Bob was safer in the cell he was locked in. Eventually, Bob managed to escape and head up to the roof for the big showdown with Kingpin, only to see the villain escape from the assembled group of heroes. Before Wade could give chase, Bob walked up to him and stabbed him in the chest with the serum.
It turns out that Tombstone really did give Bob the serum and he promised to use it for real, as Bob felt that Wade was out of control. Bob was surprised that Wade wasn't angry about his betrayal, as apparently this was all part of Wade's convoluted plan to prove that he had friends that cared enough about him to kill him. Deadpool knew Bob was the one person that cared enough to do this for him and considered him his one true friend. What Deadpool didn't account for in his grand plan to have the most epic death possible was that Bob's deal with Tombstone hinged on Tombstone being the one to kill Wade. If that didn't happen, then Bob was as good as dead. Wade hadn't considered that his death would have consequences for people other than himself.
Wade assured Bob that Tombstone was nothing to worry about but was immediately proven wrong when the villain showed up at Bob's hotel room. The two of them ran away but Bob started to slow Wade down. Thus, Wade callously pushed Bob to the ground in order to slow down Tombstone's pursuit. Fortunately, this was a ruse, for as Bob stared down the barrel of Tombstone's gun, Wade ran a delivery truck into the villain, pinning him against a wall. He helped Bob out of there, promising he would be alright, despite Bob's continued insistence that his getting whacked was inevitable. Bob finally relented when Wade assured him that neither of them were going to die.
The pair removed their costumes and dressed in normal clothes in order to safely get out of the city using a train. However, Wade's teammates in X-Force found them and Bob was knocked out by Wolverine after a pathetic resistance of throwing hot coffee at the mutant. On the verge of the lethal team gunning him down, Wade convinced them to wait to kill him until he managed to safely hide his one and only friend, Bob. When Bob woke back up, Wade assured him that he would be safe from Tombstone as long as Wade was still alive and that he meant to stay alive for a long time despite his lack of powers. Bob had finally accomplished his goal of making Wade a better, less suicidal person. [Deadpool (3rd series) #50-54]
Bob was on the toilet when Deadpool called him needing a favor, but Bob always picked up for his pal. Wade was hired to deliver to Dracula the demon lady Shiklah, his bride of a royal monster lineage. Therefore, Bob arranged to have the pair kidnapped by Hydra in their submarine and met up with them just as Deadpool had killed another Hydra agent named Bob from accounting. Before Bob could fully process this, A.I.M. showed up in a helicarrier and tractor-beamed them high into the air. When A.I.M. agents came aboard to kill everyone, Shiklah turned into a giant monster and started slaughtering all of the invaders. While this was going on, Bob and Wade had some “bro talk” and Bob soon ascertained that maybe Wade had started developing some feelings for the woman. Just as Shiklah finished off all the agents, M.O.D.O.K. appeared and froze her in a tractor beam that then started transporting everyone from the submarine to the helicarrier. However, Wade used a grenade to shut off the tractor beam and send everyone in a free fall to the earth. M.O.D.O.K. gloated that his chair could fly, so Wade stole it from him and saved Shiklah and Bob from their deadly fates. Unfortunately, Bob had a hard time holding on and plummeted from the chair to the ground, obtaining an assortment of broken bones. He was forced to recover in the hospital, but he managed to make it to the big climatic battle by way of piloting the M.O.D.O.K. chair. [Deadpool: Dracula's Gauntlet]
Bob made a few background appearances at Deadpool's wedding to Shiklah and at a roast in his honor. [Deadpool (4th series) #27, 45] He even once was knocked out and had his retinal scan used by the new Captain America, Sam Wilson! [All-New Captain America #1] He also gave Wade a heads up about a time-travel harness that Hydra was developing. However, Bob was not allowed to come on the adventure, as it was strictly a throwback team-up of Deadpool and Cable. [Deadpool and Cable: Split Second #1]
Bob got caught up in another one of Wade's enemies’ schemes when he and many other citizens were brainwashed into dressing like Deadpool and attacking people indiscriminately. After being beaten up and unmasked, Wade awkwardly had to explain to Steve Rogers why he was friends with a Hydra agent. Clutched in Bob's hand as he was loaded into an ambulance was a scrap of cloth indicating Madcap was behind the attack. Unluckily for Bob, Madcap had actually fused himself to Bob, directing him around as he stuck out from his stomach like a disgusting, sentient tumor. Bob secretly furthered Madcap's plans while hiding his secret from Deadpool. Bob even showed up for their Christmas tradition of robbing a diamond store and giving the loot to a hobo. Wade even remarked how pudgy Bob had gotten. [Deadpool (5th series) #4, 16, 18, 21]
When Madcap's plans came to fruition, he didn't account for the ineptitude of Bob. While Madcap gleefully listened in to the rage of Deadpool's partner, S.H.I.E.L.D. agent Preston, about the 
endangerment of her family, he did not realize he had been traced. Madcap smacked Bob in the balls in retaliation but was promptly puked on in response. Preston and Deadpool burst into the facility to find the Madcap-controlled Bob holding a detonator and apologizing that he had stayed silent. After blowing up the facility, Madcap leapt out of Bob's stomach to attack Deadpool directly. Luckily, both Bob and Deadpool were saved by Agent Preston. [Deadpool (5th series) #24]
Bob briefly showed up with a couple other lame villains inside Arcade's latest Murderworld, in which the players were in a fantasy style video game and Deadpool was the Unkillable Beast that could not be hurt and whose talking drives one mad. [Unbelievable Gwenpool #13] When an evil version of Steve Rogers took over America, Hydra was front and center. Bob was sent in with a few other agents to deal with an Inhuman who was destructively screaming over a grocery store's lack of Fruity Pebbles. After climbing up the side of the building, Bob couldn't figure out how to detach the “ringie-thing” on his safety cable. This was fortuitous, as the top of the building exploded and threw Bob back off the roof. He expertly used his Hydra training to alleviate the tension of his body when facing impending impact. This allowed him to be unharmed when he clumsily slammed into the Inhuman, knocking her out. [Secret Empire: Brave New World #2] When the heroes inevitably ousted Hydra as the driving force in America, Bob contacted Deadpool to tell him where they were keeping the evil Captain America, upon whom Wade was looking to exact revenge. [Despicable Deadpool #291]
Apparently, Bob was the keeper of Deadpool's keys for his many storage facilities, as he helped Wade finally locate a MacGuffin for a cosmic threat. Next, he brought in Wade on a job tip that involved WeirdWorld. Bob strategically stayed on the plane as Wade spent years trapped in the 
time distorted realm. He finally did go into action to save his friend when Deadpool finally uttered the code word “Chimichanga.” [Deadpool (6th series) #2,4] Once again being called in to act as bait for Deadpool's mercenary mark, Bob mistakenly thought they were going duck hunting together. Wade refused to let him move or eat for ten hours. Bob surprisingly managed to leave the scene just before the villain showed up to attack Deadpool. Perhaps his Hydra avoidance training had finally paid off. [Deadpool (6th series) #10]