Because klik games deal with relatively outdated technology, involving your players cuts down to the story which they must be immersed in. To make a story for your game, you must follow a series of simple steps. Although a game's playability determines entertainment, a bad story or lack thereof often ruins the experience (I know I COULD summon the Dark Magician, but why would I? Why does the fate of the universe revolve around a children's card game? WHYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY?) Anywho, moving right along...
To start making a story, you need to lay a vague backdrop, and by vague I mean leave enough room for plot twists later. For example, look at the beginning to the early final fantasy titles: A thousand years ago, good people were dominating the land. To balance it out, magic crystals gave four bad guys magical powers. They stopped the rise of good. Now, the darkness is growing, so four warriors of the light shall come. Pretty basic. Of course, you could also go with something along the lines of Dragon Quest: Your father was a royal Knight. He was on a Quest to save the kingdom from dragon whatitsface. He never returned. You, upon coming of age, must abandon your poor sobbing mother to find him. That one is kinda iffy too. However, It has a built in plot twist: what happened to the father? In the Final Fantasy story, you already know the ending. Just do what you were supposed to like the other guys a thousand years ago. Anyway, you get the idea.
The next step is the main character and his allies. For a horror/zombie/survival game, those allies probably died off already. For other games, they can range from captives (mario/peach) to allies in combat (StarFox/Falco). It is important to make the main character a strong, silent type. Keep in mind that this is the player, and so if the main character has any major flaws or is very outspoken on certain issues then a contradictory player could never experience the same story. Also, the side characters should compensate by being as outspoken as possible. The game has to have emotion without making the player feel like he can't express what he wants.
Next comes the antagonists, or villains. To make the story the best that you can, you should have three. The main evil guy, the main evil guy's pet henchman, and the other evil guy. The main evil guy has to be as bad@$$ as possible, another strong, silent type. Save your comic relief for the underling. The "Other bad guy" Is kinda outspoken, usually, and he/she is NOT ON THE SAME TEAM WITH THE FIRST BAD GUY. He could be just not in league, but it is usually better if the two have a common enemy. In matter of fact, a new ally would make another great plot twist.
Think of the original Kingdom Hearts. Melificent introduces herself right off as the main bad guy. The disney villains all have their crash and burn moments to provide the comic relief. However, the end of Melificent was no where near the end of the game. It turned out that Ansem "The Wise" and friend of the mouse was kinda possessed by a Heartless and he was the one trying to destroy the world. Melificent only died because she spread herself too thin trying to destroy you both. You just killed an ally. However, the second game reveals that she was only severely weakened. She continued to mass up the comic relief characters when a new enemy surfaced. Organization XIII, a group dedicated to finish what Ansem started, was led by Xemnas. Xemnas (reas it backwards! ) was the apprentice of Ansem. You go after both at once (like what Melificent tried to do) and eventually XIII grew too strong. Xemnas took over the witch's old castle and started fueling his ultimate weapon- kingdom hearts. It turns out that every time you kill a heartless, it feeds kingdom hearts- you've been helping him all along. Deprived of your offense, an army of heartless stand in the way between you and Xemnas. There to the rescue? Melificent. She holds her ground against the onslaught of enemies while you defeat the final boss.
Now that is an amazing example of plot twists. The hundreds of allies throughout the game are always putting their two cents worth in, but the only flaw is that the main character is way too talkative. Otherwise, KH games have a great storyline, and it actually had the disney-fantasy merge make sense. In any case, good luck on your games.