Wash and peel the onions. Finely chop one of the onions, and slice the second one.
Heat oil, and fry the sliced onions first till they turn golden brown. Take the onions out in a bowl, and let them cool. Crush them lightly and set aside.
Heat the leftover oil that was used to fry the sliced onions. Add chopped onions and fry till light golden.
Add sliced ginger and garlic paste, followed by the whole spices (cumin seeds, cloves, black peppercorn, cinnamon and black cardamom)
Cook for a minute till the flavour of the spices is released and then add the mincemeat.
Cook for 2-3 minutes till mince colour changes, and then add the powdered spices (red chili flakes, coriander seeds and salt).
Cook for a minute, and then add the tomatoes.
Cook uncovered for about 20 - 25 minutes, stirring every few minutes. Use a wooden spoon to mash the tomatoes as they soften.
Once the tomatoes soften, turn the heat to medium high and saute the qeema on high heat to bhonofy it. The qeema is ready once the oil separates (you will see oil rising to the top). The qeema will be on the dry side.
In the end, place the crushed brown onions on the qeema, along with green chilies and lemon juice. Cover the pot, and put it on low simmer for 5 minutes. This step is known as dum, and will infuse the flavours of the brown onion and green chilies into the qeema.
This Pakistani qeema recipe can be served with rice or roti as well, but my preferred way is with puri or paratha.