The apocalypse happens a lot in the video game world. Sometimes it happens prior to the events of the game, while other times, it occurs during it. While arguably overused, it's a good trope because it can lead to unique settings and stories.
What can also be fun, though, is preventing the apocalypse from ever happening in the first place. After all, there's no better accomplishment for a heroic character than stopping the planet from being destroyed. In what way the planet or universe is under threat can vary. For instance, a villain might be planning to blow the world up, turn civilians into monsters, or just wipe out civilization. Whatever the evil plan is, you can put a stop to it in these games.
5 Mass Effect 3
Throughout the original Mass Effect trilogy, you hear constant mention of a cycle of extinction. How it works is that a race of highly advanced synthetic beings called the Reapers wait until various civilizations are at their peak before coming in to wipe them out and salvage anything important. The idea is that they intervene before the organics and synthetics of a civilization destroy one another.
Unfortunately for Commander Shepard, the cycle is about to occur in their lifetime. So, you spend the games trying to stop the Reapers from arriving and doing their business. You fail in the former, but you eventually succeed in the latter, as you can stop the machines from exterminating all the Milky Way's main species in the third game. The way you do so depends on your game-ending choice.
4 Metal Gear Solid: Peace Walker
As this is Metal Gear, the situation in this one is a little complicated. The game's titular machine is an AI bipedal tank capable of launching nuclear weapons. Yet, it's supposed to be a nuclear deterrent. So, it only fires a nuke in retaliation when a country fires one of its own. The man behind the machine is Hot Coldman, who wants to prove that Peace Walker is the only true nuclear deterrence and that humans don't dare to launch nukes.
Therefore, using the machine, he sends false data to the U.S to make them believe that the country is about to get nuked. While America is considering a retaliation strike, Peace Walker is getting ready to launch. If all these nukes went off, it could've easily caused a nuclear holocaust like the ones seen in the Fallout series. However, it never comes to that as you're on hand to battle and disable Peace Walker, which stops it from launching and halts the transmission of falsified data.
3 Resident Evil 5
In the Resident Evil series, there is always a threat of an apocalypse. This is because there is always a virus going around that's transforming people into monsters of some sort. Thankfully, it never turns into an actual worldwide apocalypse because the virus is usually contained in a specific area. You're not usually the reason the virus doesn't spread further, though, no matter which skilled protagonist you're controlling.
Yet, in RE5, you actually do stop an infection that threatens to take over the world. The virus in this one is called Uroborus and is Albert Wesker's weapon. At the end of the game, the villain intends to unleash the virus on the world using missiles containing the substance. However, through a series of quick-time events and a battle with the antagonist, you put an end to his plans.
2 Witcher 3: The Wild Hunt
Throughout most of the Witcher 3, The Wild Hunt seems to be your primary issue, and they're certainly a problem. Yet, there is an even bigger threat looming in the background known as the White Frost. This is a cataclysmic event that freezes entire planets. Unfortunately, for Geralt, Ciri, and the rest of the gang, their world is the next in line to be frozen. Naturally, this would lead to the death of every living thing. So, it certainly counts as an apocalypse.
The only one capable of stopping it is someone infused with Elder Blood. This means Ciri is the world's only hope. As such, at the end of the game, she enters a tower on Undvik and permanently halts the White Frost. Technically, you can argue it isn't you who averts the apocalypse, as Ciri does it in a cutscene. But she is a playable character, so it still counts.
1 Halo 3
Halo 3 is unique becomes it contains two apocalyptic threats. The first comes from the Halo rings. These weapons were designed to exterminate all sentient life in the galaxy to stop the dangerous race called the Flood. Series villain The Prophet Of Truth attempts to activate them in Halo 3 in his delusional plan to become a god. You, with the help of the Flood, put a stop to his plans by killing him before he can fire the weapon.
Your alliance with the Flood and their leader, the Gravemind, ends there, as the species are the other galaxy-wide threat. These creatures are zombie-like as they're capable of infecting different species. Therefore, they could potentially take over everything. To stop that, you gain access to a half-built Halo installation and activate it. Because it's unfinished and outside of the galaxy, it has very little range. Thus, it only wipes out the Flood while everyone else stays intact.