This issue completes the long Protocide storyline that began behind the scenes back in issue #25 but only involved Captain America as of issue #35, which culminates in an important choice for our hero.
At the end of the last issue, in a Hydra warehouse, Protocide had defeated Cap and tossed him into the energy core Cap had just saved him from. The first sight of our hero is in the form of the stunning image below, courtesy of penciler (and writer) Dan Jurgens, inker Bob Layton, and colorist Gregory Wright.
Cap’s legendary resolve and perseverance are on display as he risks exposure to use his shield to break out and confront Protocide.
While SHIELD hits the structure from the outside, Cap bursts through from the inside, surprising only the SHIELD agent who does not know what Captain America is capable of.
Sharon tries to get Cap medical attention, but he is focused on just goal—and excessively so, letting his anger control him (as it often does, according to the Stoic philosopher Seneca, as described in pp. 55-60 of my book).
Sharon puts her foot down but it is no use against a Captain America this determined—but less manic than above, thankfully.
Cap tracks Protocide to a mountain AIM facility where he lays into the personnel—and turncoat SHIELD Agent Clete Billups, who found Protocide in first place. Meanwhile, Sharon realizes what Cap has strapped to his belt…
…the Omega Compound, a deadly biochemical weapon (from issue #35) that Cap “borrowed” from SHIELD.
While fighting his way through the AIM agents, Cap sees his recent foe Cache (from issue #34 and the 2000 Annual) before confronting Protocide once again, this time giving him no benefit of the doubt as to his true nature (as he did in the last issue).
Determined as he is but likely drained from his time in the energy core, Cap falls to a powerful blow from his enemy…
…but remains as defiant as ever.
Finally, Cap thinks of using the Omega Compound, although it is unclear how seriously he actually considers it to be a viable option. (He did bring it for a reason, though.) Although it is the easiest way to stop Protocide, he clearly realizes not only that it would mean the death of his foe and many others (including himself, which he likely doesn’t consider), but it would also have disastrous ramifications for the more symbolic and existential considerations of who he is and what he stands for.
In the end, he makes his customary assertion that “there has to be another way” before finding the will to fight back.
After he removes the helicopter’s rotor with his shield, Cap watches it fall and explode, sending flames up to where he and Protocide dangle from a collapsing platform, and now it falls on the latter to make a choice.
Protocide does reach out to stop Cap’s fall, though his motivations are unclear…
…but it is possible he heard Cap’s words, realized that he didn’t use the deadly tool at his disposal, and decided to do good when it counted the most.
Having thrown Cap out of the underground bunker to his safety, Protocide seems to have perished in the ensuing explosion, to Cap’s dismay…
…but never count a potentially good man out (although he has not been seen since).
ISSUE DETAILS
Captain America (vol. 3) #38, February 2001: Dan Jurgens (writer and pencils), Bob Layton (inks), Gregory Wright (colors), Todd Klein (letters). (More details at Marvel Database.)
Collected in: Captain America by Dan Jurgens Omnibus.
PREVIOUS ISSUE: Captain America #37 (January 2001)
ALSO THIS MONTH: Avengers #37 and Black Panther #27 and Iron Fist/Wolverine: The Return of K’un Lun #4 (February 2001)
NEXT ISSUE: Captain America #39 (March 2001)
THE VIRTUES OF CAPTAIN AMERICA 
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