Hello,
I have gone through your query and understand your concern.
You have to understand that 
Pregnancy is not only the cause for the missed period.
Your Urine pregnancy test is too negative for multiple times and you have begin spotting now.
Even stress and illness can cause the change in regular menstrual cycle and prolong your menstrual period.
Fatigue, weight gain and increased appetite may be due to some other causes like 
diabetes, 
hypothyroidism, Poly cystic 
Ovarian Disease etc.
These medical condition may be the cause for your prolonged period.
Please do the following investigation and consult a general physician.
1. Blood sugar- Fasting and Postprandial
2. Complete Thyroid profile
3. 
Ultrasound abdomen and pelvis.
Depending upon the findings, treatment varies.
Hope this helps.
Please write back for further queries.
Wishing you good health.