Amongst the numerous causes of altered mental status and severe headache are:
Bacterial and/or fungal meningitis
In altered consciousness, cerebral malaria must always be excluded since this is a common and curable infection.
Blood slide for malarial parasites
Lumbar puncture for CSF examination including Indian ink stain for cryptoccocal meningitis
Salmonella and syphillis serological tests
Blood cultures + sensitivity studies.