The ongoing debate as to whether Pluto and its satellite, Charon, comprise a double dwarf planet system or a planet and its moon was settled following the discovery that the system's center of mass and a significant portion of its mass are outside of Pluto.

A. comprise a double dwarf planet system or a planet and its moon was settled following the discovery that the system's center of mass and a significant portion of its mass are

B. comprises a double dwarf planet system or a planet and its moon was settled following the discovery that the system's center of mass and a significant portion of its mass are

C. are a double dwarf planet system or a planet and its moon were settled following the discovery that the system's center of mass and a significant portion of its mass are

D. comprise a double dwarf planet system or a planet and its moon was settled following the discovery that the system's center of mass and a significant portion of its mass is

E. are a double dwarf planet system or a planet and its moon was settled and led to the discovery that the system's center of mass and a significant portion of its mass are

Explanation:
A
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This answer choice correctly matches the following subjects and verbs in its various sub-clauses:

1 - the singular subject ongoing debate is correctly matched with the singular verb was (settled);

2 - the plural subject Pluto and its satellite, Charon is correctly matched with the plural verb comprise;

3 - the plural subject the system's center of mass and a significant portion of its mass is correctly matched with the plural verb are (outside of Pluto).

Note the the sentence's main clause is no. 1: The ongoing debated...was settled. Clause no. 2 is nested within the main clause.

B
Incorrect.

This answer choice is grammatically incorrect. The plural subject Pluto and its satellite, Charon does not agree with the singular verb comprises.

C
Incorrect.

This answer choice is grammatically incorrect. The singular subject The ongoing debate does not agree with the plural verb were.

D
Incorrect.

This answer choice is grammatically incorrect. The plural subject the system's center of mass and a significant portion of its mass does not agree with the singular verb is.

E
Although this answer choice is grammatically correct, it is illogical and radically changes the meaning of the original sentence by replacing the word following with the words and led to. The new meaning damages the original sentence's logic - because it is far more logical to say that the debate was settled based on the discovery that the mass was outside of Pluto (i.e., based on evidence), than to say that the debate led to this discovery.