Pokémon Ruby and Pokémon Sapphire are two of the best-loved games in hand-held console history. As the first Pokémon games to make the transition to the Game Boy Advance, they hold a special place in a lot of gamers' hearts. The Hoenn region brought along plenty of new Pokémon for us to catch, new areas to explore and new game functions to enjoy. Who didn't love breezing through the game with a Blaziken, or using a prize Skitty to become the champion of the Pokémon contest circuit? Of course, Ruby and Sapphire were made even more incredible by the presence of their signature legendary Pokémon, Groudon and Kyogre. Powerful is an understatement when it comes to these two!

The popularity of Ruby and Sapphire even to this day is demonstrated by the fact that the games got their own 3DS remakes, Omega Ruby and Alpha Sapphire. However, even games that are this beloved have their flaws, plot holes, and unsolved mysteries. As much as Game Freak poured hours and hours of work and ingenuity into these generally incredible video games, some issues and goofs slipped through the cracks! As is the case in a lot of Pokémon titles, there are plenty of plot points that don't make sense, Pokémon that shouldn't learn certain moves or have certain abilities, and game functions that are just plain ridiculous.

Sure, playing a game set in a totally fictional universe requires some artistic license and suspension of rational thought to be used, but there's a limit! Here are just some of the plot holes and unsolved mysteries that we spotted in Pokémon Ruby and Sapphire.

25 Diving Without Oxygen

Pokémon Ruby and Sapphire introduced a new HM into the mix for players to use outside of battle: HM08 Dive. As its name would suggest, this move allows the player to dive into the ocean and explore underwater areas, some of which featured exclusive Pokémon.

The HM added a bit more depth to the game—literally. 

However, Dive's introduction did create one massive plot hole. How did the player character manage to survive underwater without using any breathing apparatus whatsoever? Did they secretly have gills, or could they just hold their breath for hours? Nobody knows.

24 Surviving Groudon's Lair

As anyone who's played Pokémon Ruby will know, towards the end of the game the playable character has to confront (and defeat or capture) the legendary Pokémon Groudon. It can be found on the bottom floor of the Cave of Origin in Sootopolis City, waiting for you in a pit of lava. Question is, how does the playable character survive without any protective gear in what's essentially a volcano? Surely spending time in an actual lava-filled inferno of a room would have some kind of harmful effect on an unprotected child...

23 What Happened To Team Magma And Aqua?

Just like all of the mainline Pokémon games, Ruby and Sapphire feature their own evil teams hell-bent on ruining the world.

Teams Magma and Aqua each had their own incredibly flawed nefarious plan.

Of course, their missions are thwarted by the playable character and the leaders of the two teams realize that being evil might not be the best life choice. Thing is, we never find out what happens to Team Magma and Aqua after their schemes fail. By all rights, they should be in jail for various crimes—but did that actually happen?

22 Littleroot Town's Roads

This tiny plot hole doesn't really impact the plot of Pokémon Ruby and Sapphire too much, but it's still an amusing one to point out. In the game's opening moments, the playable character arrives in their new home of Littleroot Town in the back of a moving van. Thing is, the Hoenn region doesn't have any roads—especially not the tiny village of Littleroot! Does everyone just drive off-road in this place? Did the van magically teleport to Littleroot? It's a mystery...

21 Gym Leader Norman's Parenting Skills

Pokémon Ruby and Sapphire introduced a pretty interesting family dynamic into the main plot of the game. One of the game's Gym Leaders—that of Petalburg City, to be precise—just happened to be the playable character's Dad! It added a nice twist to the game for sure but also raised a lot of questions. Dad—or Norman, as he likes to be called apparently, even by his own child—seems to spend all of his time in the Gym. Does he ever actually see his wife and child? You'd hope so...

20 A Child Saves The Day (Again)

Question: do any of the regions featured in the Pokémon games actually have an effective police force? Apparently not, if the plots we've encountered are anything to go by. In pretty much every single game, a random child—aka, the playable character—is left to defeat an evil team of criminals with no help from law enforcement. Sure, Gym Leaders and other important figures chip in from time to time, but mostly, solving crimes is literally left to be child's play! Pokémon Ruby and Sapphire are no exception to this baffling rule.

19 Professor Birch's Predicament

Near the beginning of Pokémon Ruby and Sapphire, the playable character ventures onto the nearest route to their home only to find the local Pokémon professor in a bit of a predicament. Professor Birch is being attacked by a wild Poochyena, but he's left all of his Pokémon in his satchel a few feet away.

Once again, a random child is left to save the day.

If Professor Birch is such an expert on Pokémon, shouldn't he have known that venturing into tall grass with no Pokémon on hand was a stupid thing to do? Apparently not.

18 Wally's First Battle

If you're a stickler for the tiny details of each Pokémon game being totally accurate, Wally's first ever wild Pokémon battle in Ruby and Sapphire probably annoyed you a lot. Wally borrows a Zigzagoon from Norman in Petalburg City so that he can venture out and catch his first Pokémon, a Ralts. However, both of these Pokémon have flaws in their programming! Zigzagoon doesn't know Tail Whip despite being at the right level. Ralts, meanwhile, is Level 5, despite all of the wild Ralts in that area being capped at Level 4 for the player. Talk about an unfair advantage!

17 Latias Soar's Logistics

The 3DS remakes of Ruby and Sapphire—Omega Ruby and Alpha Sapphire—added a couple of new mechanics into these classic games. One of these was Latios and Latias Soar, which allowed you to fly around Hoenn on the back of one of these legendaries. Thing is, this was in no way a safe thing to do! Latias and Latios fly pretty darn quickly, and the player doesn't wear any kind of harness. Plus, surely if you were flying around that quickly you'd end up with motion sickness? Just saying!

16 Deoxys' Origins

Question: what on earth is Deoxys? This bizarre but also pretty cool legendary was introduced in Ruby and Sapphire—although it was impossible to catch unless you attended a specific event. It was apparently created when a space virus mutated, but honestly, that creates more questions than it answers. Where did the virus come from exactly? How did its mutation cause a weird, spindly Psychic-type Pokémon to come into existence? Honestly, we need Nintendo to address Deoxys' origins in a bit more detail, because we're confused.

15 Skitty And Wailord, Sitting In A Tree

Pokémon breeding is a complex and slightly odd system that involves every single breedable creature being assigned a different "Egg Group". Often, the members of each group make a lot of sense—all of the Bug-types are together, for example, and all of the dragons.

Some breeding possibilities, however, just don't make sense.

The most infamous example of this is two unlikely Generation Three Pokémon—Skitty and Wailord—being able to breed. Skitty is a tiny kitten, and Wailord is, well, a giant whale. Go figure.

14 Phoebe's Ghostly Visitor

Another addition to Pokémon Omega Ruby and Alpha Sapphire that left a lot of players perplexed was Phoebe's ghostly visitor. Phoebe is a member of the Elite Four who specializes in Ghost-type Pokémon, so perhaps we should have expected her to be involved in something spooky. However, nobody expected the ghost of a little girl to turn up in her room at the Pokémon League. Nobody knows who this girl is, or what she wants with Phoebe or the player. The whole situation is more than a little bit creepy!

13 Legendary Battling Technique

As we've already mentioned, close to the end of Pokémon Ruby and Sapphire, the player is given the option to capture a legendary Pokémon. Should you succeed in your efforts to add Kyogre or Groudon to your team, you're free to use them in battle from that moment onwards.

It's an incredibly fun prospect, but also a slightly odd one.

These Pokémon almost destroyed the world about five minutes ago—why is it suddenly safe for a child to battle with them? Besides anything else, it's just unfair on their opponents...

12 The Villainous Team's Pokémon Choices

A recurring plot hole in basically every single Pokémon game is the fact that every evil team out there uses absolutely rubbish Pokémon in battle. Ruby and Sapphire aren't exceptions to this rule! The host of Team Magma and Team Aqua Grunts that the player has to battle all have disappointing creatures like Poochyena, Zubat, and Numel. What's with that? If they wanted to succeed in their criminal efforts, they should really have chosen better Pokémon to train. It's just common sense!

11 Wally's Miraculous Recovery

At the beginning of Pokémon Ruby and Sapphire, the playable character makes friends with Wally, a kid who lives in Petalburg City. It's revealed that Wally has a mystery illness, leading his parents to send him to live with his uncle and aunt in Verdanturf Town.

It's hoped that the fresh, clean countryside air will aid his recovery.

Very quickly after he arrives in Verdanturf Town, Wally not only becomes totally healthy but strong enough to go on his own Pokémon adventure too. We're happy for him, but seriously... How did he recover quite so quickly?

10 Cutting The Grass

While the HM Cut was present in Pokémon games prior to Ruby and Sapphire's release, the Generation Three games added a new out-of-battle usage for this move. Cut now enabled the player to actually chop down the tall grass dotted around the Hoenn region. Since this grass is usually the home to numerous wild Pokémon, we have a lot of questions about this new feature. Where do all of the Pokémon go once you've destroyed their natural habitat? Is it really ethical to chop down these Pokémon's home just because random wild encounters are irritating sometimes? We'd argue not...

9 Shiny Rayquaza

There's no doubt about it: Rayquaza is one darn impressive Legendary Pokémon. However, a slight plot hole relating to this fearsome dragon exists in the original Ruby and Sapphire. Various NPCs in these games make comments to the player about Rayquaza being a huge, green dragon—which it usually is. However, it's possible to encounter Rayquaza in its shiny form at Sky Pillar, making it black instead of green. Since there's only one Rayquaza in Hoenn, how could those NPCs have seen a green one if only the shiny form exists in their world?

8 Dewford Town's "Trendy Phrase"

One of the most inexplicable features in the entirety of Pokémon Ruby and Sapphire is the Dewford Town "Trendy Phrase" mechanic. If you visit this island town, you have the option of providing a so-called "Trendy Phrase" to a boy outside of Dewford Hall. For some bizarre reason, the contents of this phrase affect where exactly on Route 119 the Water-type Pokémon Feebas will appear. What?! In what world could a phrase spoken in a random town affect the behavior of some wild fish on the other side of Hoenn? It makes no sense whatsoever.

7 Drake The Dragon-Type Sailor

Just like Gym Leaders, each member of the Elite Four in the majority of the Pokémon regions specializes in one type. Upon meeting Drake, one of the elite trainers in Pokémon Ruby and Sapphire, you'd immediately expect him to battle with Water-types. The guy dresses like a sailor, for crying out loud! It would make logical sense for a trainer with a connection to the sea to use Water-type Pokémon. So, does he? Of course not. Drake uses Dragon-types for some reason. To be fair, they are pretty cool.

6 Team Aqua And Magma's Destructive Goals

In every single Pokémon game, the grand plan of the evil team is always a little bit ridiculous and totally unrealistic. It has to be, in a way—if the plans were reasonable, you could hardly expect a 10-year-old child to thwart them. However, as schemes go, those of Team Aqua and Team Magma have to be the most ridiculous of all. They want to flood the Earth and get rid of the oceans respectively, and anyone with half a brain can see that neither of these ideas is even remotely good.