First don't refrigerate your tomatoes.
Second realize that a sliced tomato is only good for a little while, measured in minutes. Try to use it all.
These aren't The Tomato Protocol, but just a starting point to understand tomatoes.
A fresh tomato is a delicious thing; acidic, and well, acidic, and watery, not quite crunchy, full of little seeds covered in slippery delight, and wrapped in a skin at just the right chompable. Full of flavour! I don't eat them raw, it's too much-- but put a fresh tomato with something like mayonnaise, yellow mustard, green onion, jalapeno, and sure, bacon, or in a salad with a nice dressing-- now we're talking!
An unfresh tomato, like one you put in the fridge, or that has gone overripe, is bland, squishy, unpleasant in your mouth, like a pulpy dismal thing, even the seeds seem to disappear. Squalid.
This post does not deal with underripe tomatoes. In terms of The Tomato Protocol, consider underripe tomatoes to be cases not considered. It can stand in for my inexperience, since I have never eaten one, or tried to. It can stand in for humility, recognizing The Tomato Protocol does not cover all the bases. If you know about underripe tomatoes and their uses, you can expand my analogy, so it can stand in for the potential for The Tomato Protocol to expand or change in meaningful ways.
That out of the way, here it is.
Suppose you have five tomatoes. (And by the way, buy tomatoes on the vine, if you at all can. Also-- did I mention the smell? That they somehow smell like a garden? And that they have sort of an impossible to describe roughness on their smooth skin, like a thin tough fuzz that wants vaguely to fuck you up? Is it a kind of yeast, like forms on apples? Or is it just dirt? And cherry tomatoes are good to eat in alternation with salt and vinegar potato chips-- this is pretty much a secret experience that I'm telling you about...)
Back to it. Suppose you have five tomatoes. They are in various states of ripeness, all on the vine. Perhaps all on the same vine, just ripening differently, or you've got two clusters on different vines you bought at different times.
The Tomato Protocol is this: do not eat the tomato that is in danger of going overripe. Absolutely do not eat any tomato that has already gone overripe, or is going. The oldest tomato does not matter. The best tomato is all that matters. Always, always always: eat the best tomato.
Let the one that's about to go overripe, go overripe. Maybe it ends up in salsa (lime juice will revive it! I don't know why...) Maybe it ends up in the compost. But eat the best one.
The best tomato is a miracle. Enjoy that miracle. In this case, don't optimize for minimal waste, don't use the oldest first, use the best, now, at this moment, and bring true joy to your life.
This part is extremely boring, so I won't write it. Nothing can compare to the magnificence of a delicious tomato, so I don't want to spell things out, but there are other situations where The Tomato Protocol can apply.
This is not some sly reference to something obvious, I just mean what I wrote here: there are other situations where The Tomato Protocol can apply, but I don't want to ruin the zest that is now bursting in your imagination, watering your mouth, so I leave it up to you to take it any further.