When my head's too noisy... The bullets don't go where i want 'em to
Yuuji pulls the trigger, killing Kiyoka, Makina's mother. Putting an end to everything, as in Yuuji's mind, she is the cause of Makina's prolonged suffering. But due him killing someone, the seal has become undone, where once only Asako was capable of doing so due to her importance to him, Makina has now taken over her place, shattering his psyche in the process caused by the trauma he faced as a child and becomes a cold blooded killer. Shortly after, Kiyoka's guards rush to her office, hurling their bodies towards the door in a desperate attempt to break down the door. Yuuji, now deranged, unlocks the door, much to the surprise of the guards, and opens fire. A gunfight ensues in which Yuuji is able to escape from but however sustains multiple injuries as he is hit in his left thigh, shoulder and ear to the point that half of his left ear is gone and his right shoulderbones are pulverized. Later, Yuuji arrives and meets Makina as promised, much to her relief, and conveys her wishes to live with him to which he agrees to but in the end abruptly gives her a gun, leading Makina to realise that Yuuji is gravely injured. He requests her to get rid of it, returns the money that she paid for him and gives her a business card of his company, advising her to call them if she needs help and has problems she can't solve before succumbing to his injuries. With no one else to turn to, she calls the number.
In JB's words, "If any hand would to help them(Yuuji and Makina) now, it could only be that of the devil, and that devil's hand is our 'company'. A secret organization unbound by law, taking in even the most irredeemable criminals. And so long as they have potential, they will be binded with 'amnesty' and become domesticated watchdogs. A dog(Yuuji knows this very well, occasionally calling himself a dog) that's been domesticated stays that way for life. They may run away(just as how Yuuji disobeyed JB's orders and runs away with Makina), but in the end they'll go hungry and return to their kennel.(just as how Yuuji gives Makina their number for her to call). Our 'dogs' don't know how to live without a master... that's the very reason they earned their nickname."
Half a year later, it was revealed that Chiara came to help Makina. Chiara sent her to America and now Makina has replaced Yuuji as the new 9029. She is also now the owner of a small bakery and is pregnant with Yuuji's child. However, due to the fact that she blames herself, reason being that she feels that she is a burden and unable to get by alone, for causing her fathers death who died for her sake to protect and that Yuuji has suffered a similar fate because of her, and having to watch both of them die unable to do anything, she became incapable of comprehending and accepting Yuuji's death. Makina has become mentally broken, deluded and delirious to the point that she has conversations with "Yuuji", not realizing that she is speaking to a bag with a rotting body who was once Yuuji. She is telling herself that there is nothing to worry about, she can do anything now by herself and that this time she'll help him and protect him no matter what.
Instead of putting an end to everything and freeing her from her suffering, Yuuji has become the reason of her suffering.