The truth is, Kathleen had been part of Jack for a long time. Not the most important part, but a part nonetheless. Jack had known Kathleen for more than four years when he and Nathaniel attempted to take her from the grasp of the Archon. The Archon is another mysterious character. He is neither friend nor foe, but he is constant. He endures all change, and it is his will that is done in this world of Jack's (whether or not Jack approves, as we have seen).
But this is about Kathleen, not the Archon. You see, Kathleen only just recently attracted the attention of Jack. Until now, she had been nothing but a fuzzy part of Jack's memory. It all started when Jack was rereading some old sketches of his. These sketches dated back before his struggle with the Darkness, his acquisition of the White Energy, his meeting of Nathaniel, and even the cultivation of the Rose Garden.
In fact, Jack's fascination with Kathleen was fed by his memories of the Rose Garden. You see, Jack had been jaded by his experiences in the Rose Garden. The Lady of the Garden had caused him to loose faith in companionship and permanent bondage. Jack foresaw a strong and bountiful future with the Lady of the Garden, and she promised him thus. But alas, she grew tired of him and changed her mind. It took many moons for jack to realize that the Lady's words were hollow. When he did finally realize this, he revoked his trust from the majority of the people he'd surrounded himself with.
In every person, he saw the same hollowness. The same empty promises. The same selfishness. In his heart, Jack knew that not everyone was responsible, but he could not find a reason to pour his trust so willingly into others as he had before. The only one he trusted was Nathaniel. He felt thus until he stumbled upon the sketches written about Kathleen. Jack did not like Kathleen at first. He felt her to be too harsh, too reckless, too overbearing. But before long, Jack began to discover the true beauty in Kathleen. In truth, she was the most courageous, loyal, strong, sensible person he had ever come across.
Jack admired everything about Kathleen. Her personality righted every wrong that had ever been done to him in the past. She was not hollow. She made no false promises. His faith had been restored through her. It was not long before Kathleen presented herself before Jack. They spoke and were very fond of each other. Kathleen admired his reserved yet earnest personality, and Jack admired her strong yet intelligent personality. Nathaniel expressed his approval of Kathleen, and stressed that she was a one-of-a-kind companion. He did not want Jack to loose her.
This, however, was not in Nathaniel's power. It was in the Archon's. Word of Jack and Kathleen's courtship reached the Archon, and he blatantly disapproved. Nathaniel realized this, even before his master, and set off to convince the Archon otherwise. Try as he might, he could not persuade the Archon to accept a relationship between Kathleen and Jack. Soon thereafter, the Archon sent out a squad of assassins to capture Kathleen and bring her to his castle unscathed.
Needless to say, Jack was infuriated when this happened. Against his better judgement, Jack ordered Nathaniel to assist him in rescuing Kathleen from the depths of the Archon's domain. The Archon planned to permanently eradicate Kathleen. By the time Jack and Nathaniel reached her, her memory had already been wiped blank. The Archon finished his work even as the trio escaped. Indifferent to Jack and Nathaniel's power, the Archon erased Kathleen from existence.
To this day, it is unknown as to why the Archon did not approve of Kathleen. It is a grudge Jack holds against him indefinitely.