The scientific method starts with a research question. For example, does photosynthesis require light?
To address this question, you should propose an hypothesis. In this case, we hypothesize that photosynthesis does not require light.
Once we have this hypothesis, we can make a prediction. Under our hypothesis, plant does not need light to perform photosynthesis. Therefore we predict that a plant kept under darkness will behave no differently than a plant kept in the light.
To test this prediction, we design and perform an experiment. In this case, we have one plant kept in constant light, one plant kept in constant darkness, and one plant kept in natural daylight cycle. Besides the lighting, we treat those plants exactly the same. After a week, the experiment is concluded and we determine if the plant is alive or not.
Using the result of the experiment, we can test if our hypothesis is wrong. The scientific method can only prove a theory wrong, it cannot prove a theory to be correct. Any hypothesis can be proven wrong if appropriate evidence is presented, this is called falsifiability. Falsifiability is what make science science.
If we are to follow the Scientific Method rigorously, then you will have to first form a question. Instead of "the effects of the absence", consider "How would the absence of a component affect the plant?" You will then want to do some research on the functions of the different components of photosynthesis - what are they? What role(s) do they play in the larger process of photosynthesis? How do they play these roles? Then, before you go any further, you will need to narrow down and be specific about which component you want to research further.
For instance, if you want to focus on sunlight, you would ask and answer the question, "How would the absence of sunlight affect the germination/growth of a plant?", and a hypothetical answer (your testable hypothesis) might be, "Without sunlight, the plant would fail to [insert the function of sunlight here], and will not germinate/wither/develop yellow spots/[show other symptoms of illness] and eventually die." You will then test your hypothesis: You will need at least two plants of the same type, one to grow normally, and the other to grow without sunlight, to test whether the prediction you made in your hypothesis is correct, and to what degree it is correct. It is VERY important to have a normally growing plant of the same type as a control, because otherwise, you will not know whether the plant grown without sunlight was really affected by the lack of sunlight, or affected by some other factor (e.g. an insect/plant pathogen you did not detect). You will need to decide how to measure the effects of the lack of sunlight - maybe the height of the plants, how sick (or healthy) they look (perhaps by counting the number of withered leaves per day), and so on. As you observe the effects (or lack thereof), you would record your observations and data. You would then analyze the data and decide whether your experiment has tested your hypothesis adequately. If so, you can draw some conclusions about whether your observations supported your hypothesis, and look to ask and answer questions about more details of sunlight, or questions about other aspects of photosynthesis.
If you decide that your experiment did not test your hypothesis adequately, you would need to analyze why it did not, and decide how to change your experiment in order to test your hypothesis.
You would need to do an experiment in which one of the components of photosynthesis were removed and compare that to a working photosynthetic system.
You will probably need to do some genetic engineering for this, and it is likely to get complicated for several reasons, one being that not all of the components in photosynthesis are proteins so you would need to alter the downstream effects of photosynthesis, and the other being that you would need to somehow keep your non-photosynthetic normally-photosynthetic organism alive for long enough that you can study it.