Here's an idea.
So the main character (we'll call her Raven Crystal Mysteria Alexander for now unless it's a guy, at which point we can call him Raven Chris Mysterio Alexander) is an ordinary boy/girl running late for school one day. He doesn't want to be late because he's always late, and everyone picks on him for it, including the overly mean and sarcastic teacher, Mr. Doofensmirtz. All of a sudden, Raven C.M. Alexander trips on something in the road. (S)he looks up to see a shiny Victini right there. The Victini says that Raven Chris Mysterio Alexander is the only one who can save his world, so he transports both himself and the main character smack in the middle of Pinwheel Forest.
All of a sudden, flocks of shiny Pokémon come in from everywhere and all beg to be Raven Crystal Mysteria Alexander's starter, and there's this huge battle royale between all of them until only a shiny Oshawott with the ability to telepathically communicate with Raven Crystal/Chris Mysteri(a/o) Alexander is left standing. But it's badly hurt, so Raven Whatever Whatever Alexander and Victini rush to Striaton City to get Oshawott (who will henceforth be named Dewy) to a Pokémon Center where Dewy and Victini (henceforth named Tom) both decide to be Raven Yada Yada Alexander's starters.
Then Team Plasma attacks the center exactly the same way Team Rocket does in the second episode of the anime, and Raven La La La, who has previously voiced no opinion about whether or not (s)he actually wants to be the Chosen One for Unova, decides to take it about zirself to fight the forces of evil.
Insert the rest of your story here.
And that's why you should never ask a forum full of snarky and/or shameless critics for ideas.
...But seriously, if you can't think of a beginning, chances are you won't be able to think of a middle or an ending, so it's really in your best interests to think hard about how to start your own story. Besides, we can't help you here because we have no idea what your comic is about, so we don't know what kind of beginning would be best for your story. For example, if your comic will be about Team Plasma taking over the world, maybe starting in medias res with the Plasma plot succeeding might be a good way to go. Alternatively, maybe it'd be better for the story to start with the main character thwarting a bunch of Plasma grunts if your story calls for that. But if it's not about Team Plasma taking over the world, then you could have a beginning that could involve anything. Ordinary kid eventually becoming a hero? Might be best to start off with a scene of the kid doing something ordinary.
And then, we know nothing about your characters themselves. I mean, if your main character came from a family that hates Pokémon or otherwise strictly forbade the protagonist from going on an adventure (like Bianca's family did), it'd be interesting to see how they got around that. The beginning ties the character's background to the present story, so even if your protagonist doesn't have a Bianca-like personal history, who your character is and where they came from will have a huge impact on what happens in your beginning.
Point is, the first part of your comic is the foundation to your story. Asking us to write a beginning for you is asking us to write the entire story for you. We can't do that because we have no idea what you had in mind, what floats your boat, and so forth. Instead, try this. Get a blank sheet of paper or open up a blank word processor document. Write down every idea that pops into mind. Once you find a story idea that you like, start asking questions about the steps you should take to get to the parts that popped into mind. Work backwards from the middle, and you'll find your beginning.
