S’s first and last known kills are with his poisonous pen. This seems significant.
His first kill after receiving the valise with the poisons and its companion pen is in the streets of El H–. As he flees to the harbor, an assailant emerges from a dark alcove and seizes S, kicking away the valise and drawing a knife across S’s neck. S breaks free, time begins to slow, and the pen appears in his hand and he strikes out with it (p255). In a feral fight for survival, S stabs his attacker repeatedly in the neck until he is dead.
His last known kill is the Governor of the Territory, whom we now know is Pfeifer. On p353, S opens his valise and removes what he needs before hiding the case in the trunk of a tree. We learn later that one of the things he needs is his pen. One nick from the pen’s nib could stop the paralyzed man’s lungs (p362). And then finally, after struggling with just what to do with Pfeifer, he does, however, relish yet again the feeling of nib piercing skin, that tiny punch through a trivial dermal defense (p367).
Though presumably other Agents met their fate from the same nib’s puncture, nowhere in Ship of Theseus is it mentioned. In fact, the only time the the poison pen is mentioned at all is when S receives it in the valise (p247) and when he uses it twice to kill.
The pen is made, in whole or in part, with mother-of-pearl (p247). The use of pearl is always extremely significant in any story with J.J. Abrams behind it. Typically it represents the most important thing to be sought, but with it comes a crisis of faith attached on whether it is worth pursuing – on whether the choice to do the right thing is worth it any more. In LOST, John Locke faced just such a moment in a newly discovered Dharma station called The Pearl.
S’s choice to kill Pfeifer with the pen is followed by several metaphors of spiritual death (a magpie dies as he is fleeing the guard, the ship is destroyed when he finally finds it, and he wakes up in the Winter City). It is only later, as he prepares to confront Vevoda, that he chooses a different path.
What do you see as the significance of the poison pen?