Thanks to Bluemofia for his middle paragraph--mitochondria were believed to be independent organisms until being absorbed by larger ones. I'm not sure about chloroplasts, but it makes sense, all things considered.
But here's the problem--I see people saying "I believe there was one organism that everybody came from" (not picking on any one in particular). That's not science--that's just the same as claiming intelligent design. The fact is, until direct evidence is presented to support the 1-organism hypothesis, it will not become theory (note the choice of words).
There is certainly indirect evidence--the similarity of amino acids in all living things, for example, as mentioned above. However, that could simply mean that organisms using other codes of amino acids and potentially different amino acids were not as well adapted to their environments and have died out since. We have not found every fossil, every piece, of the puzzle here. Therefore, you really can't say whether or not there was a single organism to start with.
Also, that depends on your definition of life. Is a virus alive because it has RNA and it replicates itself? Are the "soap bubbles" I mentioned above alive because they regulate internal environments through homeostasis? Self-replication and homeostasis are two conditions that are typically considered to be traits of living organisms, but what if it lacks a trait? Too often, people see life as an on-off switch, when in fact there is sort of a gradient in between life and non-life.
This lends itself to the question--where there multiple paths of development? Was there a preferred route? And when do you consider something alive? We know organic molecules that are not considered living could form in Earth's history, and we know there are living things now...but where is the cutoff? We don't know enough to be certain of that.
I suppose the roundabout point of what I'm posting is that although we don't know enough about this in-between stage yet, that does not discount the theory that living things develop and change with successive generations. That is the theory of evolution and natural selection, and that has been shown time and time again in the laboratory and in real environments. Speciation among fruit flies, for example, has been observed over the last two hundred years in North America.
