The Halo franchise has long been associated with quality: engrossing gameplay, poignant music, and an epic sci-fi story. In fact, Halo: Combat Evolved was largely responsible for introducing the first person shooter (FPS) genre to home consoles with Microsoft’s original Xbox in 2001. Since then, Halo’s protagonist, the Master Chief, has become synonymous with the Xbox brand and is the most recognizable character in Microsoft’s game catalogue.

With all of its success, very few manage to point out specific flaws in the original Halo game even though they do exist. There are some plot inconsistencies that relied heavily on the expanded transmedia universe of books and graphic novels. Other plot holes were outright forgotten or waived aside by the ever-active Halo community. Ever since 343 Industries took over the mantle of responsibility of continuing the Halo franchise in 2012, several plot holes have been filled in.

Each Halo game is a different slice of Swiss cheese, and the original is possibly the most notable for having story issues. In particular, the movement and appearances of secondary characters are generally inconsistent. Some of the following points relate to confusing in-game moments, while others relate to points that have been semi-addressed over the years. Despite this, the points are all valid for players who are new or returning to the beginning of this epic series. It should also be noted that nearly all of these points carry relatively significant spoilers.

15 The Origin Of The Flood

The Flood was sealed away long ago in the Halo installation for study. That is what 343 Guilty Spark claims, at any rate. Of course, the mystery of the origin of the Flood is hinted at in the Greg Bear Forerunner novels, but never fully stated in earnest. Who sealed these Flood away if the ring was activated? How would have the Forerunners been able to seal away Flood spores if they were extremely infectious? Why would they be sealed at all? With that being said, if the Flood require food to survive, how exactly did the spores survive for so long? Were they in stasis? The mystery of the Flood is perhaps one of the darkest secrets in the Halo universe and their origins continues to be a point of lasting fascination for fans.

14 How Captain Keyes Was Taken To The Truth And Reconciliation

Captain Keyes is taken by the Flood after accidentally uncovering them with a team of Marines and Sergeant Johnson. This point is very important and will come up again. Players are not treated to a map of the Halo ring, so when Captain Keyes is taken to the Covenant ship, the Truth and Reconciliation, it is very difficult to speculate on how exactly he got there. As there is no seeming appearance of a Gravemind or higher intelligence of Flood, it is unlikely that the captain is teleported to the ship. So…how does he get there? Perhaps even more importantly: why is Captain Keyes taken to a ship when he could have been probed for information in the point of origin? Part of the reason may be a way to extend the game on Bungie’s part by having the final three missions act as recycled versions of earlier ones, but that is speculation on this author’s part.

13 Where Is Sergeant Johnson?

Sergeant Johnson: a marine taken right from the celluloid of James Cameron’s Aliens appears in levels he is not supposed to be in. During Private Jenkins’ footage of the Flood awakening, it is clear that Johnson is alive and well standing next to Captain Keyes. Curiously enough, this is the last time players see Sergeant Johnson unless unlocking the legendary ending or reading The Flood (the novelization of the game). Johnson also appears in the previous level, Assault on the Control Room, where he joins the Master Chief in battle. The kicker here is that both levels technically happen concurrently, so there is a placement inconsistency. It was later revealed by Bungie to be a re-used character model, but is non-the-less a major plot hole.

12 The Pillar Of Autumn’s Size Is Disproportional

This one is a little harder to nail down, but is very important for the sense of scale of the Halo universe. The Pillar of Autumn –a human ship– is cited on the official Halo Waypoint site to be 1.7 kilometers in length. The original game has players race against the clock inside the Autumn for a total of 3 kilometers. While the sense of urgency in the scene is constant artificially extending the size of the ship to increase the tension in the game’s final minutes is bizarre. The Autumn’s size is important as it lends credibility to the remainder of the story world and even the Halo ring itself. For a point of reference, each Halo installation is said to be ten thousand kilometers in diameter.

11 How Would The Covenant Gain Access To Cortana?

The original reason the Master Chief is paired with Cortana is to keep her away from the Covenant once the Pillar of Autumn is boarded. It is stated that if the Covenant get Cortana, they’ll find Earth. Oddly enough, Cortana later enters Halo’s network, and 343 Guilty Spark is unable to remove the index from her. Despite being a powerful and advanced A.I., Spark can do nothing except float and sputter in the wake of this upset. If a remnant of Forerunner technology cannot hack Cortana, what are the chances that the Covenant will be able to do it either? What proof is there that Cortana could be hacked by the Covenant? Even if the Chief abandoned her, Cortana could simply refuse to divulge information, and that would be the end of it.

10 Captain Keyes Can Magically Understand The Covenant

In the third mission, Captain Keyes says he ‘overheard’ two of the Covenant guards right before dumping a mountain of exposition on the player. Now, up until this point, Cortana was needed to translate the Covenant’s chatter, so what is going on here? Has the captain suddenly learned an alien language or was he trained on it previously and did not care enough to mention it to anyone? Either way, the intent of dumping a pile of lore to advance the plot does work for the overall story, but is skewed in its execution. In later Halo games, it is a conscious choice to allow the Covenant to understand English and even speak it. Unfortunately for Bungie, the Covenant never speak any English in this game, so it is very out of place.

9 Cortana Becomes Power-Obsessed In The Control Room

In a move that is seen as uncharacteristic for Cortana, she becomes obsessed with the power at her disposal when she connects to Halo’s control room. It escalates so quickly that she immediately dresses down the Master Chief, her closest ally in the fight with the Covenant. Up until now, Cortana is seen as a sly, resourceful A.I. with remarkable abilities in data manipulation and tactical strategy. She typically speaks to the Chief patiently and in a firm, but relatable manner that is born out of respect and confidence. Cortana’s sometimes-cold nature in this scene is glimpsed throughout the series, but this is the most jarring as it undermines her core relationship with the Chief. She snaps at him out of impatience, berating him like a small and insignificant person instead of the super soldier he is. This exchange feels needlessly harsh and out of place, once again creating drama without earning the respect of the player.

8 Why Was The Flood Being Studied On Halo?

It is established in the game that the Halos are the only facilities that can kill the food of the Flood, which essentially stops the parasite, killing it off through starvation. With that being said, why would the Forerunners have chosen to store samples and study this parasite on the very weapon that can stop them? On one hand, it makes sense to keep these cards close to the chest, but on the other, the risk of containment breach is too great. If this were to happen, it would become very difficult to activate the ring at all, leaving little room for error. Now, it is plausible that the Flood would be studied by the Forerunners, but why not on a closed-off environment that could be closely monitored at a safe distance from the Halo array?

7 Cortana Could Be Taken By 343 Guilty Spark When She Connects To The Autumn

Near the end of the game when Cortana and Chief return to the Pillar of Autumn, Cortana briefly takes control of the ship to destroy it. 343 Guilty Spark appears, disabling the ship’s automatic destruct and downloads the summary of human history. At this point, it would have been very easy for Spark to simply download Cortana from the Autumn in order to retrieve the Index. The rules here are fairly ambiguous. Why is Spark unable to take Cortana when he can easily access all systems aboard the ship? One would think that the writers would maintain defined rules consistent throughout the world. Unfortunately, this point is a major oversight given that it could have been remedied with a simple exchange between the Chief and Cortana.

6 Private Jenkins Should Be A Flood By Now

When the Master Chief is sent to stop Captain Keyes from uncovering a weapons cache, he encounters the body of Private Jenkins. The body is locked inside of the room where the Flood is first discovered. Despite this, Jenkins is not infected. Why is that, exactly? It is the mandate of the Flood to consume all life in the galaxy. If Jenkins was killed beforehand, the Flood probably would not want to infect his corpse. However, we have video evidence courtesy of Jenkins’ helmet camera that he was overwhelmed and killed by the Flood. So, the plot hole is either that the Flood did not infect Jenkins by choice or they killed for sport, which does not make practical sense. Unlike Sergeant Johnson, Jenkins is never recognized as having immunity to the Flood, so this is a large inconsistency.

5 The Halo Ring’s Differing Environmental Terrain

If the Halo ring was built to study the Flood, why would it have several different environmental conditions in it? Throughout Halo: Combat Evolved, we experience rocky terrain, grassy canyons, valleys of ice and snow, swamp lands, an island in an ocean, and sprawling desert. With so many varied locations on the Halo ring alone, one can’t help but ask the question why these varied environments exist at all. Through the Forerunner Saga of novels by Greg Bear, we learn that the Halo rings have life in order to re-populate the universe of indexed species thousands of years after the rings are fired. So, if life were to evolve again, why have all of these environments? Why not keep the pleasant ones consistent around the ring?

4 Where Is The Covenant Leadership?

What kind of direction does the Covenant have in this game? It is explained that Halo has deep religious significance to the Covenant, which is a perfect motive for them to occupy the ring. With that said, we never get to see the Covenant leadership in Combat Evolved. Their motives are only ever hinted at in broad strokes via Cortana. Of course, in the follow-up, Halo 2, we learn that the Elite eventually anointed as the Arbiter was in charge of the operation on Halo and is blamed for its destruction. Across the games, it feels like too quick of an explanation. It would have been fascinating to see the Arbiter as the commander of that fleet and in his prime. In fact, the original title is extremely light on Covenant lore, focusing primarily on the mystery of the Halo.

3 Foe Hammer’s Resurgence

In the final level, Foe Hammer, humanity’s most reliable Pelican pilot, answers a distress call to rescue the Chief and Cortana from the exploding Pillar of Autumn. The last we heard of Foe Hammer, she attempted to rescue the Chief after the Flood are unleashed. For two whole levels, we don’t hear any mention of her, and suddenly Foe Hammer breaks radio silence and re-appears to save the day. Well, she tries to save the day. Where has she been amidst the chaos of unleashed Flood? Maybe she’s been idling in the air. It seems odd that we hear nothing at all until the very end of the game. How has she survived for so long only to be shot down (conveniently) when the Chief finally needs her to pick him up?

2 Disappearing Marines

This one could have a very simple answer or a very complex one based upon the point of view. In Combat Evolved, the Marines disappear a bit. Actually: they disappear almost entirely after the level introducing the Flood. From this, are we to assume all Marines died or mutated into the Flood in the second half of the game? It seems possible that this was the case for many of them. Did others evacuate themselves? Did some make a last stand against the overwhelming odds of their attackers? We know Johnson and a small team of marines escape the ring because of the novel First Strike. What about the remainder of the crew? It would have been good to see some closure on this thread even though we know that at the end of the game, everyone still on the ring is dead.

1 No Covenant In The Library?

If the basis for the Covenant’s interest in the Halo rings is for religious significance and they wish to activate them, then why didn’t they make an appearance at the Library? It can be assumed that they attempted to traverse the intricate maze and were overrun by the Flood. Players can imply that the Flood you fought in the library are actually mutated Covenant. However, it would stand to reason that some would still be alive or more would appear due to the importance of their ‘Great Journey.' Given that they would need the Index to fulfill this religious rite, one would assume and by not attempting to do so seems like a missed opportunity on their part. Of course, this is aside from the fact that only humans can retrieve the Index and activate the rings – a fact that Guilty Spark is well aware of the entire time.