Top 5 Mysterious Pokemons

1.Ash greninja

     It first saw Ash when he was kicked out of the Prism Tower in Kalos, Where Dreams and Adventures Begin!.

 It continued to observe the gang until Team Rocket intervened in Ash and Clemont's friendly Pokémon battle. It volunteered to help out by successfully using its Frubbles to counter Jessie's Wobbuffet, but ended up receiving quite a bit of damage during the encounter. Ash then decided to take it to Sycamore's lab, where it was treated and restored to full health. 

While leaving Professor Sycamore's laboratory the next day, Froakie threw a chunk of its Frubbles in Ash's face in order to get his attention. It was standing alongside a Poké Ball on the floor in front of it, expressing its desire to join his party. Froakie then happily pressed the Poké Ball's button and was caught.

It evolved into frogadier in the episode A stealthy challenge.

and it evolved into Greninja in the episode a festival of decision while protecting pikka chu from bisharp, after evolving it suddenly synchronized with ash . they strongly synchronized in the episode championing a research battle and eventually ash become unconcious.

They mastered this mysterious power in the episode seeing the forest for the trees while saving spupa.later they used this mysterious power to beat the ice gym leader vulfric.

2.Ho-oh

Ash first saw Ho-Oh in Pokémon - I Choose You!. It appeared in a forest on his way to Viridian City during his first day as a Trainer. He was lying on the ground with his injured Pikachu and saw it fly over the rainbow that appeared in the sky after a storm. His Pokédex could not identify it and explained that many Pokémon were still unknown.

In Pokémon Emergency!, Ash tried to explain to Professor Oak what he had seen, though the image he used to point it out appeared to be of an Articuno rather than Ho-Oh. Either way, Professor Oak did not believe him and brushed it off as Ash being mistaken. This gold-colored version of Ho-Oh was an early concept of Ho-Oh as a Pokémon, as it, like all other Generation II Pokémon at that time, had not been fully developed yet.

The topic was brought up again in A Ghost of a Chance. While Ash was in Johto, he explained his encounter to Eusine, who also did not believe that Ash had seen this Legendary Pokémon. In For Ho-Oh the Bells Toll! they heard the bells in the Tin Tower ringing, which would signal Ho-Oh's approach. At this point, Eusine was so upset by Ash's claim that he challenged him to a battle.

As fate would have it, Ash saw Ho-Oh a second time in Gotta Catch Ya Later! after he parted ways with his close friends Brock and Misty. The third time he saw it was in Battling the Enemy Within! after May pointed to it flying in the sky after Ash lost an informal challenge against Pyramid King Brandon and was released from possession by the King of Pokélantis' spirit.

It appeared in a flashback in Dawn Of A New Era!. After making amends with Dawn, Ash recalled seeing Ho-Oh on the day his journey began.

It will appear in the 20th Pokémon movie.

 3.The crystal onix

The Crystal Onix  is a special Onix with a body made out of glass crystal.

The Crystal Onix's first and only appearance is in the anime episode The Crystal Onix. Ash and his friends first heard of it through a note they found in a bottle floating in the ocean. The note was written by a little girl named Marissa. She wanted to find the Crystal Onix to help her brother, Mateo, gain inspiration to make glass Pokémon statues. Mateo told a story of how his grandfather discovered the Crystal Onix and then was able to make extraordinary sculptures afterwards. One of those sculptures included the Crystal Onix itself.

With the help of Marill, Tracey was able to assist greatly in finding the Crystal Onix's hideout.

Besides being made of crystal, the Crystal Onix is also unique from other Onix in that it can live in water without being hurt by it. Its glass skin also gives it a special resistance to Water-type attacks.

Mateo realized that he would have to use a different type of attack to weaken it and so, he used his Charmeleon and attacked it with Fire Spin. It seemed to have a weakness to Fire-type attacks, unlike other Onix. Mateo was just about to capture it when he realized that he didn't need to. Just battling it gave him the inspiration he needed to create glass Pokémon sculptures. He thanked the Crystal Onix as it submerged itself into the water once again.

4.Shining noctowl

 Noctowl debuted in Fowl Play! where it flew to a bird house. Dr. Wiseman was trying to capture the Noctowl using traps rather than Poké Balls, but each time Noctowl outwitted him and escaped the traps — usually leaving him hypnotized in the process. Ash was offended by Wiseman's tactics and plotted to capture Noctowl traditionally.

 Wiseman hypnotized Noctowl using its own Hypnosis by a mirror, but Noctowl managed to escape,  just in time for Team Rocket to attack and attempt to capture it. Ash risked his own safety to make Team Rocket's mecha claw open and allow Noctowl to fly free, before Noctowl marshaled the power of Totodile, Cyndaquil and Pikachu to destroy the mecha and send Team Rocket blasting off.

Following the rescue, Noctowl challenged Ash to a battle. Dr. Wiseman decided that it was too smart for him to catch, so Ash should have a go. Pikachu was hypnotized and began to use Thunderbolt on everything except Noctowl. When he shocks himself, he returns to normal. Cunningly, to avoid further hypnosis, Pikachu closed his eyes and listened for Noctowl's wings, then used Thunderbolt, knocking Noctowl out and allowing Ash to capture it.

5.Golden magikarp

         

      In the episode 22 of the series XY ash and his friends on their way to the sellaur city decided to visit the ambrette aquarium. where they met an old man who told them about the golden magikarp.

According to the local legend the golden magikarp had saved a man drowning in the sea. The old man was trying to catch that golden magikarp to complete the aquarium’s collection. Ash and his friends decided to help the old man to catch the golden magikarp. On seeing this the team rocket also wanted to catch that golden magikarp. So, they painted their magikarp submarine into gold, soon their submarine was caught in the fishing poles of ash and his friends. after a battle the team rocket was blasted off again. Finally The old man, ash and his friend were able to see the golden magikarp at the end of the episode.