This should fix most of your problems:
@echo off
title %name% - The Fishing Game V 0.2(alpha)
color 0f
pause
echo --------------
echo AlexSoft Copyright-2013
echo --------------
pause
color 0c
echo ERROR LOADING TFG.mp3
pause
color 0f
echo __________________
echo.
echo ~THE FISHING GAME~
echo.
echo __________________
echo.
echo (Future ASCII ART HERE)
:options
echo Type New to start game, type exit to quit.
echo Type Plan to view planned ideas.
echo Contact me: (TBA)
echo Remember, as of V 0.2, you cannot save the game!
set /p you=">" goto checkmenu
:checkmenu
if %you%==new goto Gamestart
if %you%==exit goto closecmd
:end
:Gamestart
@echo off
cls
echo You are waking up
pause
echo You are up
pause
echo You yell hello
pause
echo No response.
pause
echo You don't remeber what happened, how you got here, or even your name.
pause
echo Then you think about how you need to survive.
pause
echo You arn't trained to survive in the wild.
pause
echo But then you remember, you're not trainined to do anything, heck, you arn't even 'trained' to know your name.
pause
echo You say to yourself, "Now what?"
pause
echo To start making a shelter, press A
echo To look around for any others, press B
set /p you=">" goto checkshelter
:checkshelter
if %you%==A goto A1
if %you%==B goto B1
if %you%==a goto A1
if %you%==b goto B1
:end
:A1
cls
echo You look around for a good place to make shelter.
pause
echo You find a good spot under a large rock for sleeping, but its too narrow to make a shelter in.
pause
echo To make a shelter here, Press A
echo To keep looking, Press B
set /p you=">" goto checkmake
:checkmake
if %you%==A goto A2
if %you%==B goto B2
if %you%==a goto A2
if %you%==b goto B2
:end
:B1
cls
echo While looking, you were attacked by 2 wild wolves.
pause
echo You have died...
pause
ping localhost -n 2 >nul --> what is the point of this line?
goto options
:A2
cls
echo Once you're in, you feel something large on your leg.
echo.
echo It turns out that hole was a home to a nest of scorpions, which, so far luck for you, havn't attacked.
pause
echo You slowly move out safely.
pause
echo but your not safe
echo They have swarmed out of the ledge and you run
echo Though you dont know that it is the animal instinct is to kill something running from you, because only prey would run from you.
pause
echo As you may have seen where this is going, you felt a sharp pain in your leg.
pause
echo To great relief, it was only a thorn.
echo But, while you take that thorn out, a scorpion is under you.
pause
echo This time it stings you...
pause
echo You have died...
pause
ping localhost -n 2 >nul --> What is the point of this line?
goto options
:B2
cls
echo Sorry, this is as far as we have scripted!
echo.
echo retry for a different story/ending!
pause
ping localhost -n 2 >nul
goto options
:options
cls
echo here is where your options would be if it was scripted
pause
exit
:closecmd
exit
I have made bold what I changed, and italicized a line for your answer. I would also add more "cls" so that the user doesn't have to look at tons of text at once. Easier on the eyes.
Let me know if you have any questions.