Anti-slavery individuals and institutions during the Founding advocated for prohibiting the slave trade and abolishing the institution altogether.

The delegates would end up prohibiting congressional interference with the slave trade for twenty years (Article I, Section 9, Clause 1). 

As the twenty year mark was coming closer, President Thomas Jefferson wrote in his 1806 annual message to Congress: "I congratulate you, fellow citizens, on the approach of the period at which you may interpose your authority constitutionally to withdraw the citizens of the United States from all further participation in those violations of human rights which have been so long continued on the unoffending inhabitants of Africa, and which the morality, the reputation, and the best of our country have long been eager to proscribe. Although no law you may pass can take prohibitory effect until the 1st day of the year 1808, yet the intervening period is not too long to prevent by timely notice expeditions which can not be completed before that day."

Ironically, Pinckney's idea of South Carolina banning the trade was unfulfilled as his state was the only one left that did not ban the slave trade on its own.  Most Southern states faced a surplus slavery population, so they were willing to ban the trade.  However, the debate in Congress was not always easy.  One draft of the ban included violators forfeiting their slaves to the federal government, and Northerners did not want the federal government to be slave owners.
Annotated by bacraig on August 06, 2014
On this same day, the Confederation Congress passed the Northwest Ordinance.  The document outlined the process for admitting a new state in the Union north of the Ohio River.  There is a popular assumption that there was some grand bargain between the Convention and the Confederation Congress that included Northerners agreeing to the three-fifths clause and in return, Southerners accepting the slavery ban found in the Northwest Ordinance.Historian George Van Cleve argues that the three-fifths clause was not part of any bargain, but it was that the North abandoned support for negotiations with Spain to give up navigation rights of the Mississippi River that helped Southerners agree to a slavery ban.Also, in Article VI where the ban was written, the issue of fugitive slaves was left open.  It said "There shall be neither slavery nor involuntary servitude in the said territory, otherwise than in the punishment of crimes whereof the party shall have been duly convicted: Provided, always, That any person escaping into the same, from whom labor or service is lawfully claimed in any one of the original States, such fugitive may be lawfully reclaimed and conveyed to the person claiming his or her labor or service as aforesaid."

See George Van Cleve, A Slaveholders' Union: Slavery, Politics, and the Constitution in the Early American Republic (Chicago: University of Chicago Press, 2011).
Annotated by bacraig on July 15, 2014

This is, covertly, the second mention of the three-fifths clause at the debate.  Wilson and Hamilton’s motion, if it had ultimately prevailed, would have meant that both Houses of the legislature would have been proportional, and both would have counted slaves at a ratio of three-fifths.  Considering how contentious both of these issues would later become, it is remarkable to note that this motion did initially pass, albeit narrowly, and with almost no argumentation.  The states that had voted for the rule in the first branch but against it in the second branch (Maryland, New York, and Connecticut) almost certainly did so because they objected to the Senate being assessed proportionally, not because they objected to the three-fifths rule.  In order to follow the tortured route that the three-fifths clause took on its way to adoption into the Constitution, follow the votes taken in:  (Paragraphs 458, 461, 1229, 1251, 1260, 1289, 1293, 1314, 2078, 2092, and 2702).

Annotated by luzzell on September 05, 2013

This is the first vote on the three-fifths ratio in the Constitutional Convention, and there are a few significant details worth noticing.  First, the motion was seconded by Charles Pinckney of South Carolina (which is understandable), but it was initiated by a Pennsylvanian, which seems strange given the prevalence of anti-slavery sentiment in that state.  Second, the rationale originally given for the ratio was that it conformed to the ratio that the Confederation Congress had already almost adopted for the purpose of requisitioning taxation (even though the ratio here would be used for a very different purpose – apportioning representation).  Third, there was only one objection to this rule when it was first advanced, by Elbridge Gerry of Massachusetts.  And fourth, it passed overwhelmingly in this vote by the Committee of the Whole: 9 to 2.  It is possible, too, that the dissenters (New Jersey and Delaware) objected more to the idea that the rule for apportioning representation would be proportional rather than the fact that slaves would be counted at a ratio of three-fifths.  This issue would later become one of the more virulent battles within the Convention, but it is clear that the theoretical implications of the three-fifths rule was not immediately apparent to most of the participants.  In order to follow the tortured route that the three-fifths clause took on its way to adoption into the Constitution, follow the votes taken in:  (Paragraphs 458, 461, 1229, 1251, 1260, 1289, 1293, 1314, 2078, 2092, and 2702).

Annotated by luzzell on September 05, 2013