You have only one independent clause here because you have a single subject governing a single albeit compound predicate comprising three verbs joined with conjunctions.
Here’s a parse of your sentence’s constituents:
(S (NP He)
(VP (VP took
(NP the money home))
and
(VP was
(VP (ADVP subsequently)
arrested
(PP on
(NP unrelated charges))))
and
(VP is
(PP now)
(PP in
(NP prison))))
.)
As you see, there is just one S node, so exactly one independent clause.
There are any number of ways of writing this, depending on what you are trying to emphasize in its phrasing, but not all are equally felicitous.
- He took the money home and was subsequently arrested on unrelated charges and is now in prison.
- He took the money home, was subsequently arrested on unrelated charges, and is now in prison.
- He took the money home and was subsequently arrested on unrelated charges, and is now in prison.
- He took the money home, but was subsequently arrested on unrelated charges and is now in prison.
- He took the money home but was subsequently arrested on unrelated charges, so is now in prison.
- He took the money home and was subsequently arrested on unrelated charges, so is now in prison.
- He took the money home and was subsequently arrested on unrelated charges so is now in prison.
As you see, I suggest mixing up your conjunctions a bit instead of sticking only to and, because using but or so with these can make this easier to read and understand, and possibly to phrase.
As my previous sentence illustrates, there can be good reasons for using a comma before the conjunction even when it does not begin a new independent clause — the sort of thing one might use a dash for, but less obtrusively.
You might also prefer later over subsequently here.