Unfortunately, there are quite a few diagnoses that are relevant to muscle soreness and weakness beyond a week’s span. Be sure to have a physician examine you to at least rule out some of the more basic physiological diseases.
Once those are cleared satisfactorily, ask yourself the following questions:
Was there a precipitating event? That is, did it happen all of a sudden? If so, how?
Where in the body did the pain originate? What was the quality of the pain (sharp/burning/dull & aching/sore/tingling/numbness)?
How long did the pain last?
If the pain began with a precipitating event (e.g. “I lifted something;” “I slept funny;” “I twisted in the shower;” “I leapt to catch a ball;” etc.), it usually indicates a sprain or strain to muscle, tendon, or ligament. If you hear a “pop” or “crack” in a joint, it is most likely a connective tissue rupture. If this is the case, you will need a good interview by a sports medicine physician (MD/DO) and probably a scan of some kind (x-ray or CAT scan for bony/cartilage tissues; MRI for muscle/tendon/ligament tissues). This will help to determine what damage, if any, has been done, and if the issue warrants surgery and/or therapeutic intervention. This needs to be your first port-of-call for pain lasting longer than 1-2 weeks.
Once you have determined that there is minimal damage, and therefore, that surgery is unwarranted, you can determine that the cause is one of the following:
Not normal delayed onset muscle soreness (lasting 24-72 hours): See my answer to What causes delayed onset muscle soreness?
A sprain or strain: See Sprains, Strains and Other Soft-Tissue Injuries
If there are multiple areas around the initial location of pain and injury, you may have developed myofascial pain syndrome: “Myofascial pain syndrome typically occurs after a muscle has been contracted repetitively. This can be caused by repetitive motions used in jobs or hobbies or by stress-related muscle tension. While nearly everyone has experienced muscle tension pain, the discomfort associated with myofascial pain syndrome persists or worsens.”
Myofascial pain syndrome (Mayo Clinic)
As a bit of an aside, sub-acute (1-6 months) and chronic (more than 6 months) of myofascial pain are treated thus:
“A successful treatment protocol relies on identifying trigger points, resolving them and, if all trigger points have been deactivated, elongating the structures affected along their natural range of motion and length. In the case of muscles, which is where most treatment occurs, this involves stretching the muscle using combinations of passive, active, active isolated (AIS), muscle energy techniques (MET), and proprioceptive neuromuscular facilitation (PNF) stretching to be effective. Fascia surrounding muscles should also be treated, possibly with myofascial release, to elongate and resolve strain patterns, otherwise muscles will simply be returned to positions where trigger points are likely to re-develop.
The results of manual therapy are related to the skill level of the therapist. If trigger points are pressed too short a time, they may activate or remain active; if pressed too long or hard, they may be irritated or the muscle may be bruised, resulting in pain in the area treated. This bruising may last for a 1–3 days after treatment, and may feel like, but is not similar to, delayed onset muscle soreness (DOMS), the pain felt days after overexerting muscles. Pain is also common after a massage if the practitioner uses pressure on unnoticed latent or active trigger points, or is not skilled in myofascial trigger point therapy.” (Wiki: Trigger point)
(PS – I’m really proud of the Wiki on this. They nailed it, spot on.)
In a standard clinical interview, you have to go over all the aforementioned patient history, physicians’ reports, scans and anything else you can tell or show the practitioner about what may be the cause of the pain. Your practitioner can then figure out what muscles do the motion that produced the injury & other perpetuating factors, which allows the practitioner to decide what to treat first. This is the general clinical starting point for therapeutic focus.