Normally, I am pretty adept at picking out grammar problems, but I am stuck on this one. Word 2007 flags the following sentence as incorrectly using the word “come”:
" The mission statement guides the company in everything it does, so it only makes sense that it **come **first in your presentation."
World suggests that I use “comes.” That doesn’t sound right to me. Survey says…?
comes is correct.
“It” is a singular subject. It requires a singular modifying verb “comes”
coke comes in boxes.
replace coke with “it”
it comes in boxes.
“Come” is correct. Word is not picking up that you are using it as a subjunctive (to make a suggestion). The sense is “so it only makes sense that it [should] come first in your presentation.”
The third person present indicative is “comes;” the third person present subjunctive is “come.” Word is giving you the correct form for present indicative; in the sense you mean it the present subjunctive is correct.
That’s the adjective I was looking for to describe this usage, “subjunctive.”
To quote Wiki
It’s vestigial in English, and becoming more so every day, so much so that it is often not recognized when it occurs.
As written, the sentence talking about something that exists as a critique. Its written as “does come” which becomes “comes” when omitting the does.
If you want to use subjuntive, add a ‘-ould’ or similar word as demonstrated.
Word’s grammar check was written by software experts, not grammar experts.
My take on it is that “come” is correct because it is subjunctive. It’s a conditional, potential, hypothetical assertion – in terms of what is physically possible, the mission statement need not come first – it’s a question of a rhetorical choice – and you are giving an argument as to why it ought to be placed first.
Past subjunctive differs from past indicative only when “to be” is present: “If I were you…” Present subjunctive, which is called for here, is much rarer in English, but hardly obsolete. “She suggested that he have the honor of representing us all.” Not “…he has…” (indicative) but “…he have…” (subjunctive).
It appears to me that the OP is making a recommendation about a presentation that has yet to be written, not making a critique on a presentation that already exists. In the latter case the indicative would be correct; but that does not seem to me the sense of the sentence.
“Should” is not really required; the fact that the OP is making a recommendation is evident by his use of the subjunctive alone (come).
you read it differently than I, but I can see your interpretation.
in my opinon, as a professional writer, when writing for business, include the “optional” words, omit the redundant ones (like “that”).
Contemporary English does seem to prefer “should” or a similar word to the bare subjunctive, but it’s still a regularly used form.
True. Inclusion of “should” would have made the sense of the sentence and the correct verb form to use clear.
The OP is not a subjunctive. It’s is not conditional at all. Let’s remove the introductory clause (which is irrelevant):
“*It only makes sense that it come first in your presentation.”
What is conditional about that? It only makes sense that it is indicative mood.
Unless you’re in the UK, where, I am informed, the jussive subjunctive is quite obsolete. The clause would go “it only makes sense that it comes first in your presentation” or “it only makes sense that it should come first in your presentation” (or an alternative modal form, such as must or ought to).
If we’re just going to start tossing out phrases and words that we decide are irrelevant, I would submit that come is misspelled in this context…
Seriously, though, the introductory phrase is not irrelevant because that’s what the second half of the sentence is conditioned on. A paraphrase would be “Because the mission statement is important, it should come at the beginning of the presentation.” This paraphrase makes it clear that the second clause is conditioned on the first.
The sentence could be recast into the indicative but it would lose the connection between the importance of the mission statement and its place in the presentation, which connection I think is the whole point of the sentence.
Maybe I am misunderstanding you here, but the sense is the same whether you use a modal verb or not. In North America, you would use “come” in either case if you are making a general suggestion to someone about a presentation that does not yet exist or that you have not seen.
If you are responding to something that does actually exist, then the indicative is appropriate.
Yes, in the US, all those forms (“it only makes sense that it come/comes/should come first”) are synonymous. A writer is free to choose whichever one he delights in.
In the UK, the jussive subjunctive (“that it come first”) is very seldom used these days, but I will have to leave it to the Brits here to weigh in on whether they would call it merely archaic or actually non-standard.
I don’t know about “archaic”, but it sounds formal and yes, a little old-fashioned. Not incorrect or non-standard, yet.
Thanks, everyone, for all of the helpful information. I’m surprised that this phrase generated the interest that it did.
The context, in case anyone is curious, is an email I was sending to my students regarding their performance on project presentations this week. I teach a discussion section of a production and operations management class in which students have to create a fictional start-up company. The first part of the presentation has to do with introducing the company, hence the mission statement comment.
I don’t think any of them will notice the “come”. 
I would use “come”. It is not a conditional, it is a traditional subjunctive. The subjunctive has disappeared in England, as I discovered when an English copy editor flagged several dozen of them in a book I coauthored that was published in England. Since I had the last say, I just ignored those flags. In North America, I suspect that “come” would come readily to anyone my age, but it may well be disappearing here too.
I think the most important comment is that there is no definitive answer to the question.
I hate grammar check because of stuff like this. I know how to use uncommon moods and tenses. Well, at least better than some computer programmer with an Elements of Style in his well protected pocket. Occasionally, it reminds me if, in my haste, I’ve forgotten a comma (or something similar), but I never take it at its word when it tells me I’ve made a grammatical mistake.