At first, it was revealed by Gin that the APTX 4869 was a poison to kill people who know too much about the Black Organization. He used Shinichi as a guinea pig. Shiho Miyano said that she didn't intend to create a poison, which suggests that APTX 4869 was originally developed with a different goal in mind. It probably was just a useful side effect that the current prototype kills while leaving no trace in the victim’s body, and was thus employed as a poison - a usage which Haibara detests. Additionally, APTX 4869 is nicknamed the "incomplete detective" by the Black Organization, which means its true purpose has not yet been achieved.
Immortality/anti-agingEdit
One possibility is that the goal of the APTX 4869 is to develop a therapy which will cause immortality, stall or reverse the effects of aging, or extend a human's lifespan. The de-aging effect that occurred when Shinichi and Haibara took APTX 4869 probably indicates the main intent of the drug's development. After Pisco saw Haibara shrink back to her child form, he commented that he was impressed she had developed the drug to that point, implying that deaging is in the right direction.Supporting this is Haibara’s line, "Kudo-kun? You would probably never even dream that you are already part of a project the Black Organization has been working on already for half a century." APTX 4869 is the only known intersection between Shinichi and the Black Organization; meaning that Shinichi's de-aging made him relevant to the Black Organization's project.
According to Haibara’s description about APTX 4869, APTX 4869 activates telomerase, an enzyme which can increase the number of times a cell can divide, and therefore affect a cell's lifespan and “reproductive potential”. The goal of this might be to revert all non-neural cells to a "youthful", high reproductive potential state. Vermouth's unnatural youth is another indicator that the Black Organization may be involved in research towards extending lifespan, halting aging, or rejuvenating the body.
The goal of the antagonists in Magic Kaito is pursuing immortality, via the Pandora Gem, but it is unclear whether if the organization in Magic Kaito is the same one as the Black Organization.
Raising the deadEdit
The original purpose of APTX 4869 might be to raise the dead. Once when Conan asked Haibara directly what APTX 4869 was meant to do she replied, "It's a nostrum to raise the dead. I wonder if that answer is satisfactory?" The context of the comment, however, makes it unclear if she was merely bluffing to provoke Conan into revealing that he had been looking into the Black Organization behind her back, rather than making a serious statement of the purpose of the drug.
"Silver Bullet" and "APTX 4869" are two names for the same projectEdit
In a flashback, Shiho recalls the end of the recorded message left by her mother which revealed Elena had been working on "a truly terrifying drug" the Miyano parents called the Silver Bullet. It is unclear whether Silver Bullet is the Miyano parents' personal nickname for what is currently called APTX 4869, or if it was a closely related project they developed in parallel. Whatever the case, Silver Bullet and APTX 4869 are probably closely linked if not the same in-development drug. Haibara took over her parents' research after they died, with the APTX project named specifically. After watching Haibara shrink, Pisco, who knew about the project the Miyanos worked on, commented that Shiho's parents would be proud of the progress Shiho had made on the drug. In addition, Haibara had earlier referred to APTX 4869 as a dream-like drug. the same expression Elena's labmates used to describe Silver Bullet. During her recollection of the tapes, Haibara was holding and considering the antidote to APTX 4869. She then regrets that she didn't understand the drug was something that should have never been made, strongly implying she worked on the same drug as well. Lastly, Vermouth, who was in the Organization long enough to have heard the Miyanos use the name "Silver Bullet",may have given Conan the same nickname in reference to his deaged state caused by the drug.