The OED says this:
4. colloq. Usually with the. The state of nakedness, the nude. Frequently in in the (also one’s) altogether.
The expression appears to have been popularized by the novel Trilby by G. du Maurier, although in that context ‘the altogether’ appears strictly to mean ‘(a portrait of) the full body’ (as opposed to the face, hands, etc.), with the idea of nudity being secondary or implicit.
[1894 G. Du Maurier Trilby I. i. 25 ‘I’m posing for Durien the sculptor, on the next floor. I pose to him for the altogether.’ ‘The altogether?’ asked Little Billee. ‘Yes—l’ensemble, you know—heads, hands, and feet—everything—especially feet.’]
1894 Nation (N.Y.) 59 311/1 The dislike..of Trilby’s posing for the ‘altogether’, doesn’t jibe with the author’s authoritative declaration that to all artists..‘nothing is so chaste as nudity’.
Green’s Dictionary of Slang has an 1890 citation which seems to confirm the OED’s contention that it primarily meant the whole body, rather than naked:
1890 [UK] A.J. Vogan Black Police 193: A certain yellow tone of colour [...] pervades the ‘altogether’ of the old man, for the iron-rust and clay-stains of years of lonely toil [...] have dyed the skin.