Need help/advice regarding removing the rear wheel/tire

[p-man_imp]

First absolutely great day here temperature-wise to go for a good ride. Got home from work, got on my gear and hopped on my bike and notice it was very heavy to move. Side stand and off the bike and the back tire is flat. Put it up on the centre stand and rotated the rear tire and there is an f'n screw in my tire. Do i need to take the tire off or can i get a repair kit and plug it? If i need to take the tire off, what is the process regarding the chain, brakes, etc. I'm not an idiot but i have limited experience turning wrenches. Any help would be appreciated.

thanks,
Paul