I think you are looking for too narrow of an answer when you ask,
"Does the darkness of the later work reflect a general descent into
darkness in his personal life?"  You're assuming that the thoughts
expressed in the "dark writings" were the product of (reflect) a unique
personal experience, but I would argue that most were more
profoundly influenced by societal changes that he directly involved
himself with during his last years.  His views were not unique though
his expression of them, especially in fiction, often was.  In the United
States, anti-imperialists' fears about the consequences of imperialism
were amplified by the contemporary preoccupation with the
millennium, with imperialism interpreted as a distinct break with the
past and a danger for the future at a time when reviews of the 19th
century and projections of the 20th were a focus of attention.

That attention to the millennium began shortly after Twain's accute
period of grief over Susy's death was coming to a close makes the
two influences difficult to disentangle when dealing with Twain alone,
but the influence of imperialism and the millenium are easy to identify
in the writings of others who did not suffer personal losses.  Here are
some brief quotes from personal letters written by others involved with
the Anti-Imperialist League that might give you a broader perspective
on such works as the "Eden and the Flood" series in _The Bible
According to Mark Twain_, "Eddypus, The World Empire," "History
1,000 Years from Now," "The Stupendous Procession," some of his
letters and speeches, and other writings dealing with personal and
political disasters and their consequences.

Charles Eliot Norton to Leslie Stephen, June 24, 1898:

The days are grave and disheartening, and the prospect is dark.  We
have been living in a Fool's Paradise, hoping that in the long run the
better elements in our national life would get the upper hand, and that
we should stumble along, with many a slip indeed, but on the whole in
the right direction.  But the war has suddenly roused us from this
dream.  America has rejected her old ideals, turned her back on her
past, and chosen the path of barbarism.  All the evil spirits of the Old
World which we trusted were exorcised in the New, have taken
possession of her, and under their influence she has gone mad.

Charles Eliot Norton to E. L. Godkin, Dec. 31, 1901:

It has been, for the most part, so wretched a year in public affairs as
to afford but a dark background for domestic happiness.

Gamaliel Bradford to W. G. Sumner, March 11, 1899:

I have stored up a good hope till this war.  But now my courage has
collapsed.  I have always predicted that unless we changed our
course this was coming but had no idea how soon.  At present I rest
under the fearful conviction that by the year 1950 this country will be
governed by a military ruler at Washington.

Moorfield Storey to E. L. Godkin, Jan. 15, 1900:

I feel very confident in the end our views will prevail.  What I dread is
the series of calamaties which I fear my country must suffer before the
people will realize the truth and awake from their dream of conquest.
I have great hope that the realization is begun but the haute finance is
against us and is very powerful.

Moorfield Storey to George F. Hoar, Feb. 28, 1900:

To me the nation seems face to face with the gravest question that it
has ever encountered.  The policy of the Administration in my
judgement is sure to involve this country in the very gravest difficulties
and to result in the overthrow of self-government in this country, not
perhaps in twenty years or fifty years, but certainly in the end.

Moorfield Storey to C. E. Norton, Oct. 22, 1902:

The times are in many respects so evil that I fancy some sort of a
revolution may come, but when and how is not clear.

Winslow Warren to C. E. Norton, Oct. 22, 1902:

We appear to have lost all that differentiated us in principle from the
land grabbers abroad and to have entered upon a conquering course.
Some great disaster or a gradual appreciation of the fact that it wont
pay is all I fear that can change the popular tone.

Elwood S. Corser to Herbert Welsh, Nov. 7, 1900:

I feel that the American people have closed the gates which have
heretofore been opened to all, by which we had access to the best
conditions a people have ever enjoyed on this planet.  Democracy
has passed, and a  pitiless, conscienceless, plutocracy reigns.  We
shall reach a final good, but how and when and what suffering
intervenes, who can say?

Louis R. Ehrich to Carl Schurz, May 16, 1901:

The whole Nation is wallowing in a slough of selfishness.  I fear that
some great National calamity will be necessary to make our people
appreciate the fundamental facts of public virtue and of National
righteousness.

Winslow Warren to William Lloyd Garrison, Jr., May 16, 1900:

The moment we began to talk about the "little brown men" and
"niggers" and to justify our course towards the Filipinos on the ground
that they were an inferior race needing Anglo Saxon domination we
threw away the results of the Civil War, went far towards justifying
slavery and approved the action of the South since the war.  We have
already abandoned the theory of universal suffrage and the idea that
a semi-civilized people must educate itself to freedom by its own
experiences and efforts and are now upon the English ground of
conquest and subjugation.

Jim Zwick