Bullet wounds, broken bones, and illness (disease) aside, one simple reason for pain may be improper (or less than ideal) use of muscles.
I was asked for some stretches for the achilles. The person asking had limited ability to flex the foot upwards which has always limited their ability to squat.
Is stretching what they need?
Now I'm a big fan of stretching. However, when it comes to "stretches", I don't really teach stretches. What I teach instead is muscle control.
An advantage of muscle control is that it isn't reliant (not completely anyway) on a position or particular stretch.
And ironically (or perhaps tellingly) if you've got something like tight ankles, it could mean that you've got muscles that can't activate when they need to.
So is it a stretch you need or do you need to practice turning on (and off) particular muscles?
Why might achilles tendon tightness be a symptom of inactive or non-functional muscles?
One reason is to protect a joint or joints.
If you assume that ligaments aren't passive but active, i.e. affected by muscle activation, then that can lead to the idea that muscle tension can then affect joint capsule tension (since ligaments tend to attach to joint capsules.) Why is this important.
If you can add tension to a joint capsule (or control tension) that means you can control joint capsule fluid pressure.
Say your bones are being squeezed together. With muscle activation you can tighten the joint capsule to resist articulating surfaces from pressing against each other. You can basically create and maintain space between articulating surfaces, and here's an idea, help provide better lubrication (since the parts aren't rubbing, or at the very least aren't rubbing as much.)
So what has this to do with a tight achilles tendon?
To maintain "necessary" joint capsule tension, different muscles are going to have to come into play. If one muscle can't play, that means joint capsule control is potentially limited, which means that lubrication can be affected.
In addition, if lubrication is affected, that means articulating surfaces will rub and that in turn can mean that parts of the joint capsule may be subjected to excessive tension. Over time this could cause a joint capsule to rupture.
Then you have no control since lubricating fluid is no longer contained.
Now, do you think joints are critical structures or non critical?
If you've ever watched any war movies, a key way to hamper the enemy is to cut of supply lines. And one way to do that easily is to blow up a bridge. Bridges are hard to replace (especially if they are over a deep gorge or river.
We tend not to think of joints as critical structures until we need one replaced or can't use it for some particular reason.
Now imagine you're god, or nature, or you have the experience of eons of evolution. Do you think you'd program the brain to look after joints (since they are critical structures) or not?
(This assumes that the brain controls our muscles. If it isn't, then substitute in for brain whatever it is that controls our muscles.)
A lack of flexibility may not mean that you need to stretch. Instead it could mean that you need to learn to activate a particular muscle or muscles.
If you've had an injury (or simply never learned how to use your body effectively, or picked up bad habits from your parents or other people you are close to) you simply may need to tell your brain that a particular muscle is available for use.
Note that this isn't to say that stretching isn't bad or that you shouldn't do it.
However, in cases of pain or poor function, it may be a good idea to look at muscle function first, or at least include some sort of muscle control in your training regime.
So what would I suggest for a painful achilles?
Rather than stretching the ankle, look at using it.
Sitting in staff pose (sit upright with legs straight out in front… lean against a wall if this is difficult), start by wiggling your toes.
Feel your feet as you do so.
You can even focus on feeling your shins.
Next, practice bending your feet forwards. Repeat a few times.
Then try bending them backwards.
Next practice turning your feet inwards and outwards.
Here again notice the sensations.
You can try repeating these actions while bending forwards.
Another simple thing you can do is turn your feet in and out, and focus on feeling your heels as you do so. Try to feel your heel moving.
Staff pose with feet turned inwards
Once you can do that, next try to stiffen your heels. You should find that the tendons at the front and back of your ankles stiffen as you do this.
(You should also notice muscle activation along the sides and even the backs of the shins).
Note, notice differences between feet. You can focus on one foot at a time.
Try to adjust one foot so that when you do each of the above exercises both feet (and that includes feet, ankles and shins) feel the same.
Note, you probably won't get them feeling the same. Nonetheless, try to adjust without forcing.
If you've ever had to tune in to a radio station then this is the same idea.
"Adjust" means making small and slight movements. It also means moving slowly and smoothly.
Standing upright you can try bending the feet upwards, one at a time.
As a compliment, lift your heels.
Wow, your heel lift is nice!
Notice movement of your hips relative to your feet as you do this.
Repeat in a forward bend.
Initially you may have to shift your hips rearwards to lift your forefeet. As you get better, try shifting your hips forwards.
You can also try the same action in downward dog. Rather than pressing your heels down, focus on pulling up on your forefeet.
Note that the feet are fairly complex. It's taken me a number of years to get my feet sorted (and I started out with collapsed arches.) So be aware, the exercises described above may help, or they may work initially but then you find other problems.
The two main exercises I'd suggest for now are spreading the toes (try that while standing!) and heel activation.
If you still have problems, then there are more foot exercises that you can do but you may also have to look at hip (and thigh) muscle control also.