Ultimate Spider-Man

The animal patterns on the samples are a lizard, a rhino, a vulture, and a scorpion. This would mean that Spider-Man would fighting his foes who would take the samples.

The USS Excelsior is a reference to Stan Lee, and his famous catchphrase "Excelsior!"

One of the names on Coulson's list of replacements for Flash as Spider-Man is Miles Morales. Miles is the current Spider-Man in the Ultimate Spider-Man comics.

Mac Porter, CEO of Damage Control, is designed to look like Dwayne McDuffie, comic book and television writer and creator of Damage Control, who passed away on February 21, 2011 due to complications from emergency heart surgery.

While posing as a Zodiac agent, Spider-Man gives his name as Dan Ditkoberg. This is a homage to Dan Ditko, one of Marvel Comics' most revered artists.

When speaking with Spider-Man, Thor refers to Agent Coulson as "Son of Coul," a play on the term "Odinson," which refers to a son of Odin. Coulson was previously refered to in a similar manner by Thor in the 2011 live action film Thor.