Pokémar Episode V, A Clone's Destiny

The Story So Far...

Alex Russet and his partner Thunder are the leaders of Team New Hope, renown heroes of Unova Minor. Years ago they prevented Armageddon by destroying the Bittercold. And since that day they've done all they can to help the world. Things were good. Things were peaceful.

And then the world fell apart.

The Temporal Tower, the place where Dialga watches over the flow of time, collapsed. The resulting blast riped the land apart and brought time to a stop. Some were lucky and were still able to move in this wasteland. Most were not. Only Alex and Thunder out of all of New Hope managed to avoid this fate. 

Alex had taken a glancing hit from the shockwave, altering him and transforming him back to his natural human form as well as giving him a new trick, dimensional screams. The ability to see the past or future upon touching an object. The only good thing to come from this disaster. Life became a constant battle for survival. Dwindling resources and the inability to grow food quickly led to the collapse of society. A truly dark time. 

Eventually they came across a Grovyle and a Celebi with a plan. Using Celebi's time travel abilities they would send a team back before the disaster and have them take the five time gears to the Temporal Tower to reset it, thereby undoing the apocalypse. Together the group hunted down the gears in the current timeline so they'd be ready to go when they went back. However Dialga, having been driven to primal madness, struck during their mission. Their flash cannon struck a time gear and Thunder was seemingly killed. Alex mourns the loss, but is forced to move on.

Eventually, all five time gears are located and Celebi prepared to send Alex and Grovyle back in time. Their efforts were brought to a halt after being confronted with Dialga and their newest underling, Dusknoir. Alex and Grovyle barely made it out, but the time portal was struck by a blast in the fight. The now unstable portal separated the two of them, wiping Alex's memories and transforming him into a Treekco in the process. Alex was sent into the sea and washed ashore on a beach, meanwhile Grovyle continued the mission.

On the beach Alex is rescued by a Pikachu who asked for their help in joining the Wigglytuff guild. Alex agreed and forms Team Shock-Leaf with them. Over the next few months the two of them explored the uncharted continent of Sinnoh Minor, eventually stumbling across the time gear plot, incorrectly assuming Grovyle meant harm.

Being led on by Dusknoir, pretending to be an ally, they confronted and captured Grovyle, after which Dusknoir revealed his true colors. Now with the truth and a revelation that the Pikachu was, in fact, a mind-wiped Thunder, they set off to finish the mission. 

In the end they were successful, but the success came with a cost. Everything, and everyone, from that dark future was unwritten from time. Thunder, trip through the time stream had altered him enough that he wasn't affected, forcing him to watch Alex vanish before him.

Time passed and Thunder tried to move on with little success. One day after visiting Alex's grave he saw none other than Alex himself, but not the Alex he remembered. This was Alex of the present day. Who had never seen the end of the world and traveled back in time. He had seen the present day Thunder vanish. Two different people with two different sets of memories.

Alex and Thunder face an uncertain future, fearing that their relationship will never be the same...