Fun with Star Trek! What I caught:

AndrAIa sports a tricorder.
The alert sounds at the end mimics the Red alert in TOS
The crew and their "mission." (An obvious one!)
The doors in the Principal Office open and close exactly the same way, with exactly the same sound, as the old Enterprise doors (swoosh!).
Robert Cursor talks...in..a..very..familiar..way.

My "nit-picks" are as numerically proceeds:
1) Some of the Heroes do not have hover-boards when they depart for another Spectral hunt. Is this intentional? Speaking of which, from where did the Heroes acquire their hover-boards? Are hover-boards mandatory for all systems? What if a system is 3-bit and its inhabitants do not recognize the existence of hover-boards, as was displayed in the episode "Enzo the Smart?" Moreover, from where did Enzo Matrix and AndrAIa acquire their hover-boards? They had not left Mainframe with hover-boards. In fact, they were paraded into the game within a hover-car that greatly resembles the one pertaining to Bob.
2) To where did AndrAIa leap after she intimidatingly inquires, "Oh yeah, and how are you going to stop me?", with her trident emitting a blinding light. I had not noticed any ledges or overhead platforms.
3) That muscle-bound female Hero is clasping the Spectral virus. However, it vanishes after the Spock-like Hero subdues the Spectral virus. Did the muscle-bound female Hero drop the Spectral virus?
4) AndrAIa's icon is in game Sprite mode during the conclusion. Why? Had she not transposed her icon to default mode so as to remain after a game's completion? If she did not do so, then how exactly is it that she does not leave with the game?
5) There is a Star Trek VI: The Undiscovered Country reference at the very conclusion as represented by a Spectral assuring Enzo Matrix and AndrAIa that Spectrals and Heroes intend to reach a peace acquiescence, even if it is not accomplished until the next generation. A resemblant statement was whispered to Capt. James T. Kirk by the Klingon emissary who is later assassinated in the aforementioned motion picture.
6) Is it just me or did that one Hero capable of dispensing icy powers, such as freezing the Spectral virus, remind any one of a certain character in Killer Instinct? By the way, how does existing as a living popsicle enable one to fly? The same applies to half of the other Heroes presented as flying.

[message edited due to insulting comments regarding the moderator--this being me]

The writer of this episode was D.C. Fontana, who also wrote the TOS episode "Journey to Babel."

AndrAIa articulates, "Hatred and prejudice never is," to a Spectrol. However, the two nouns result in the word are rather than is, as is instructed by proper grammar.

I think I found three new refrences. First, AndrAIa says that Matrix and her have a prime directive. In Star Trek they also have a prime directive. Next AndraAIa says "make it so" which is said in Star Trek a lot. Finally when the Spectrol says something about the next generation. Since they seemed to only make refrences to the original series maybe they were making a conment about Star Trek the Next Generation.

D.C. Fontana was a regular script editor on the original Star Trek. Also, who voiced the "leader" spectral? I think it was James Doohan.

Tons of Star Trek homages in this one, beginning with AndrAIa's log voice-over and Glitch emitting a tricorder sound effect.

The members of the hero selective say they have the ability to reboot, but none appear to wear clickable icons, or each one's is unique.

Capt. Robert Cursor wears something that looks a lot like a key tool on his left forearm.

The Stanley Cup is on display in the Heroes' Den.

AndrAIa wears her standard (rebootable) icon right side up for a change, and then inverted in later scenes. Later again it is seen in game sprite mode without having been clicked.

I checked but did not see any voice talent credited that I remember from Star Trek.

Was anyone else reminded of the Organians from TOS when they saw those balls of light?