Training to be a ninja begins with the basic, then works up to the advanced. It's like trying to build a building. You don't start with the top because then it would fall on the boss that you really do love...
Anyways, all training for anything starts with the simple, in this case, basic strength building. On the page linked below, it gives the basic strengthening exercises and stretches that can be begun with. Even if you all ready have the basic strength to accomplish great feats of ninja prowess, it's still a good idea to continue doing the basic exercises so that you won't go the way of the retired athlete (muscle to flab). So have fun training, but remember to be careful; never go past your limits.
You want to begin with stretches so that you can warm your body up. Just think, a Starburst candy is hard to chew cold, but if you work it back and forth, eventually, it will be warm and much easier to chew and mold. I recommend that you work through all of these stretches.
Start by stretching your fingers. Push them gently backwards against your palm.
Gently press your wrist downward, then upward.
Carefully twist your wrist around.
Swing your arms over your head, first slowly, gradually working up to a faster speed. Work forward, then backwards. This warms up your shoulders.
Pull your arm across your chest and pull on it with your other arm. Do this to both arms. This also warms up your shoulders. It also stretches out your arms.
Drop your arm behind your back and, with your other arm, push down on your elbow. This stretches out your shoulders.
Move your rib cage side to side. Do this by moving your torso to the side while leaving your hips and lower body motionless. Start slow, then speed up a little. This and the next exercise warm up your torso.
Move your rib cage out and in. Do this by first sticking your chest out, then collapsing it in.
Put the soles of your feet together, wrap your hands around your ankles, then pull your feet towards yourself. This and the next two exercises warm up your hips and inner thighs.
Bend forward and touch your nose to your toes. Then bend forward from your hips, keeping you back straight.
Touch your nose to your knees. Do this for both knees.
Stretch your legs out straight infront of your self and point your toes away from your self. Pull your arms straight up and sit up straight for a bit. This warms up your back, legs, and hips
Stretch out and bend forwardm keeping your back straight, hold for a bit, then relax and grab your toes. This and the next stretch stretch out the backs of your thighs and the back of your knees.
Take one hand and grab the foot opposite to that hand. Stretch your other hand out to the side or behind you, which ever you can do better with out hurting too much. Do this for both sides. This stretches out your back.
Pull one foot in to your self and stretch the other leg out straight to your side. Grab the foot of your straight leg with your opposite hand. Do this for both sides. This stretches out your side/back.
Stretch both legs out to the side until you feel a stretch on the inside of your thighs. Then lean forward and try to rest on your elbows to intensify the stretch. This and the next two stretches stretch out your inner thighs and hips.
With your legs in the same position. Lean to a side with the top arm reach towards your toes that your head is pointing towards. Reach the other arm towards the other toes. Do this on the other side, as well.
Kepping your legs in the same position, lean over one leg such that your stomach is over your thigh. Grab the nearest foot with both hands. Do this for both sides. This stretches out your leg.
Stand up with your legs spread about the distance of the width of your shoulders. Lean forward and place your hands on the floor infront of yourself. Hold this position for a minute. This begins the stretching of the backs of your legs.
While remaining bent over, reach over to one foot and grab the ankle. Pull yourself towards the leg. Do this for both sides. This stretches out the leg that you are bending over.
While remaining bent over, reach between your your feet to a spot just behind yourself. This fializes the stretch of the backs of your legs.
Finally, sit down and roll your ankles in slow circles until they feel warm and loose.
Now that we have warmed up, we can start doing some exercises. Do each of the exercises 15 times to start with. If, after doing 15 of them, you don't feel anything, add five more until you feel a slight burning in the muscles being worked.
Turn your feet parallel, then bend your knees while keeping your back straight, like you're sliding down a wall. This warms up and works out your legs, mainly the fronts of your thighs.
Spread your legs apart to about the width of your shoulders. Bend your knees so that they go out wards, like a frog. Don't go all the way down. Go as far down as you can before your heels pop up. This exercises the inside of your thighs.
Put your feet together, parallel again, then go up on your tippy toes. This exercises your calves and ankles. If you can do this on a step, this gives you a much better work out.
Stand next to a wall for a support. Rest your back against the wall, then kick your leg forward without bending it. Turn so that your side is resting again the wall, then kick your leg straight up with your knee pointing to the ceiling. Finally, turn around and put both hands against the wall and kick your leg backwards, your knee pointing at the floor. Remember not to let your knee bend. These work your leg muscles and your gleutius muscles.
Push-up time! You can either do it with your legs straight, your toes resting on the ground, or you can band your legs such that your knees rest on the ground. This exercises your pectoral and upper arm muscles.
If push-ups come too easily for you, go into a hand stand against a wal (so you won't lose your balance) then bend your elbows. This is one of the ultimate strength exercise, something I wouldn't recommend you start out with.
Lay with your back on the floor and your knees bent. Rock forward such that your shoulders come off the ground. Start with your legs bent, resting on the floor. After a set, lift your legs up, like you are sitting on a chair. After another set, stretch your legs straight up. This exercise works your abdominal muscles, both lower and upper. The ultimate goal with these is to get to over a hundred of them.
Lay on your back again, like you did for the previous exercise, with your legs bent up. Sit up until your elbows touch your knees. This exercise works your abdominal muscles. If you can do fifty of these easily, you need to add weights of some sort. You could start with two cans of vegetables held inyour hands, held next to your ears.
Rest such that your stomach is flat. Rest your hands and feet on the ground like you are going to do the crab walk. Bend your elbows and allow your hips to drop slightly. This exercise works the opposite side of your arms from the side you worked with push-ups.