- Crowning Moment of Heartwarming, when Schala returns, causing Magus to question his beliefs (followed by the typical reaction that occurs in fanfics when they reunite.)
- Crowning Moment of Awesome: An enraged Max shoots himself up with a syringe full of now-deceased Samus's blood. Next chapter, Ridley is totally destroyed by someone wearing the Varia suit.
- Any time Link actually gets an opportunity to do his job, he soon starts being taken seriously.
- The climax of Ridley's Last Stand, when Max defeats Ridley with nothing but the Power Glove.
- so, he just killed a dragon with his (almost) bare hands?
- amazing, isn't it?
- The fact that Max set out for Ridley's station despite being completely unarmed and stripped of his gear. Sure, he ended up with Link in tow, but he didn't know that setting out.
- Why didn't Megaman just go with him?
- "I AM BOWSER!! KING OF THE KOOPAS!!"
- "What are you gonna do with that gun, kid?"
- Crowning Musicof Awesome: Unusual given that there's no actual background music to what is a series of text documents. However, Word of God has stated that several scenes, and even entire chapters have appropriate musical counterparts.
- The above Crowning Moment of Awesome, for example, was written with the end credits of Super Metroid in mind.
- Max and Crab building their Bamboo Technology? Original Brinstar theme. (appropriate, given the chapter is closely tied to the episode "Metroid sweet Metroid", which used the same song in a seriously crowning moment.)
- The entire ending of the first book, starting from the narrative on Ridley, is the ending credits to the original Metroid.
- In a notably non-Metroid example, the museum "stage" Megaman ventures through: it's Yakogoro Eirin's theme from Mega Mari.
- Salamander's "Poison of Snake", during major conflicts. This is a Shout-Out to Captain N: The Game Master's use of the "Fortress" theme from the famicom Gradius II.
- Complete Monster: Ganon, whose first known casualty in the series is a small child
- Fridge Horror: It is subtly implied that both Max and Samus are hiding mental problems brought on by unfortunate pasts. Both have been dealing with them since childhood, but taking into consideration just how old Samus really is...
- Les Yay: Peach is not too subtle about her attraction to Samus.
- Moral Event Horizon: Max eventually shot and killed Solid Snake for getting on his nerves, although the whole thing was retconned from existence by the Reset Button below.
- Damara Attempts to take advantage of Gaia's deserted state at the end of Ridley's Last Stand to invade it claim it for the Federation. It takes a call from Chairman Keaton himself to put a stop to it.