Part 5: Secondary Operations
Rather than taking his anger out on Cable, Bastion instead made good on his threat to potential mutants. During his operation in the mansion, Cable had telepathically warned Nate Grey of Bastion’s threat to their “family,” the Greys, family of their “mother,” Jean Grey. [Cable (2nd series) #46] Unbeknownst to Cable, Bastion’s technology included devices capable of intercepting such telepathic transmissions and the head of O:ZT dispatched two Prime Sentinels to murder Jean’s niece and nephew, Joey and Galen. Upon returning to the Hulkbuster base in New Mexico, Bastion monitored the operation with reluctant approval when the Sentinels reported success. However, unknown to him, Nate Grey had intervened and used his prodigious telepathic abilities to create the illusion of the children’s demise. [X-Man #30]
Though having traveled from New York back to New Mexico, Bastion arrived in time to witness the arrival of the five captured X-Men, a scene which he shared with a clearly troubled Jubilee. However, Bastion himself was slightly troubled as he considered the unconscious prisoners. Clearly still having no memory of his past lives, Bastion took a moment to consider why his hatred for mutants ran so deeply, a line of thought he just as promptly abandoned. Returning to a sensation of glee, he then showed Xavier images of his captured disciples, questioning him gloatingly if he ever thought his dream would end like this. As the pieces of Bastion’s plans proceeded, he himself had little to do but wait.
While his hackers continued to work on the decryption of the Xavier Protocols, Bastion spent his time goading Xavier, testing whether his telepathy had really been lost or 
whether Xavier had been lying all these weeks. However, even as Bastion gloated, his best laid plan was unraveling. While being locked away in a prison specially designed for him, Wolverine had regained consciousness and overpowered his guards. Donning their armor as a disguise, he subsequently freed the other four X-Men. Bastion quickly learned of the escape and began to coordinate their recapture, confident that their escape was futile, as he had sealed the base. However, having been kept nearby as a source of mocking, even in a straightjacket Jubilee was in a position to unseal the base and allow the X-Men to escape. [Wolverine (2nd series) #115, X-Men (2nd series) #66-67]
Though clearly unhappy that they had escaped, Bastion did not seem greatly intent on their recapture. Either he assumed that their escape into the desert was not much of an escape, or that in the great scheme of things their freedom meant nothing to his plan. Instead, he merely ordered Daria to prepare transportation for him back to the Xavier Institute. As it happens, this seems to have been the final order Daria carried out on his behalf. Having been a loyal and invaluable assistant, Daria had
developed a connection with Jubilee and had been having misgivings on her treatment and captivity. Herself a Prime Sentinel unit, Daria had managed to break her core programming and in turn decided to break Jubilee of her bonds. Enabling her Sentinel implants, Daria flew Jubilee into the desert. However, when other Prime Sentinels gave pursuit, Daria set Jubilee safely on the ground and flew on as a decoy, eventually self-destructing and making her pursuers believe that both she and Jubilee had perished. [Generation X #29-31]
The betrayal of his assistant Daria, even after the Prime Sentinel transformation process, must have caused Bastion to take the time to verify the loyalty of his operatives. 
In such a process, Bastion discovered that the head of a squad of First Strike troops, Commander Ekaterina Gryaznova, was a double-agent, who had been planted to spy upon Operation: Zero Tolerance. As punishment, she was transformed into a Prime Sentinel for later use. [X-Force (1st series) #82]
Possibly the result of so many betrayals, as well as the subsequent escape of Jubilee, Bastion’s interest in recapturing the five escaped X-Men increased, as en route to the Xavier Institute Bastion ordered the activation of sleeper Prime Units in the area, despite the fact there were only three nearby. As it happened, however, the X-Men were right next to the three sleepers, having stumbled upon the nearby locals who had been the unwitting test subjects in the creation of Prime Sentinels by the Prospero Clinic. Despite the subjects’ sudden transformations, the X-Men quickly prevailed, preventing them from reporting their location to Bastion. [Wolverine (2nd series) #116]
Bad news continued to be received by Bastion on his flight to New York. Agents had reported that Israeli Mossad agent Sabra had just arrived on US soil with intelligence obtained from her country regarding Bastion and his more covert activities. His demeanor turning to panic, Bastion contacted Agent Harper at the Prospero Clinic, to order the activation of more Prime Sentinels. However, even before his arrival at his destination, Bastion learned that the clinic had been overrun by the five X-Men, who had already learned of the clinic’s secret. Bastion’s trip to the Xavier Institute took a slight detour as the first hint of good news reached him. Though Sabra had indeed made contact with one of the X-Men, namely Iceman, it seemed their first destination was the recovery of Timothy Jones, son of Detective Charlotte Jones. Months before, Detective Jones had gained the ire of Bastion, who no doubt over the intervening time had learned of her short-lived romantic relationship with Archangel of the X-Men. As a result, operatives of Operation: Zero Tolerance had kidnapped her son, to use as bait for Iceman. However, though the ruse had worked, he escaped with the help of Cecilia Reyes and, joined by Marrow and Sabra, avoided recapture by Prime Sentinels. [X-Men (2nd series) #66-68]
Now, however, Sabra’s intelligence caused them to converge on a house in Connecticut where Bastion had sequestered the kidnapped Timothy Jones. Upon their arrival, the four mutants were immediately surrounded by Prime Sentinels. Once again in charge, Bastion could not help but gloat once more. 
Further, he imparted personal information that perhaps he had only begun to recall himself. He informed Iceman that he was once not unlike them – less than human. He recalled being cast before a judgmental god, who deemed him worthy and transformed him into a man to defend his fellow man against mutants. He explained that the lady of the house, Rose Gilberti, who had been seeing to Timothy during his abduction, had taught him what it meant to be human. However, hearing this proclamation, Rose rejected Bastion, asking if his current actions reflected what he had learned from her. Clearly, she saw nothing of herself in Bastion’s actions, a statement which visibly stunned the man. [X-Men (2nd series) #69]
Taking advantage of the stunned Bastion, Marrow launched an attack, which ignited a battle between the mutants and Prime Sentinels. Bastion himself began to trade blows against 
Iceman, easily holding his own in the battle. However, it was Iceman who ended the fight, not with a victory but by surrendering in order to prove a point. Bastion had claimed that he was fighting to save humanity, however it was Iceman’s contention that with every mutant Bastion killed he was taking one step farther away from that same humanity he was so desperate and determined to defend. To this end, Iceman offered his own life. As noble as Iceman’s intentions, his point seemed lost on Bastion, who immediately began to order the X-Man’s execution. Unfortunately for Bastion, it was at this moment that operatives of SHIELD arrived, revoking Operation: Zero Tolerance’s rights to operate on American soil.
Unbeknownst to Bastion, Senator Robert Kelly, one of the country’s foremost proponents of human rights against the mutant threat, had become disillusioned with the policy behind Operation: Zero Tolerance. Some hours before, he had met with the White House and, with his advisement, a policy shift had occurred. Surrounded by agents of SHIELD, 
Bastion knew that all of his planning and preparation, all of his international machinations and all of his illegal experimentations were at an end. As such, he did the only thing he could do – and surrendered. So ended Operation: Zero Tolerance.[Wolverine (2nd series) #116, X-Men (2nd series) #68-69]