This is a "Siamese Twins" crossword: there are two distinct fills for the same grid, and their clue lists are merged together, and you have to figure out how to divide the clues to fill the grid consistently both ways. There are two twists: (1) One fill has cryptic across clues and non-cryptic down clues, and the other has cryptic down clues and non-cryptic across clues. (2) There are three entries (marked with exclamation points!) for which only one clue is given: 25 Across, 26 Across, and 16 Down. Each of these clues can be read as a cryptic clue whose solution can be entered into one fill of the grid, but also its surface reading is a non-cryptic clue for the corresponding entry into the other fill.
So, by figuring out which clues are cryptic and employing ordinary crossword strategy, you fill in the grid both ways. There are exactly ten grid locations that have the same letter under both fills; they spell out THIRTY-FOUR, read from top to bottom. The two entries at 34 Across are DUCK and WEED; so the answer to the puzzle is DUCKWEED.
The people in the main theme are CASTOR/POLLUX, who are identical but not conjoined, and JEKYLL/MRHYDE, who are conjoined but not identical. Further, all pairs in the crossword are related but somehow opposed: CASTOR is mortal while POLLUX is immortal, CHANG is across while ENG is down, JEKYLL is good while MRHYDE is evil, and one crossword has cryptic across clues while the other has cryptic down clues.
Solutions to the clues follow, in the order given.
ACROSS:
1. CHANG (non-cryptic)
1. ELBOW: WOBBLE reversed - B[alance]
4. DATSUNS: US STAND anagram
4. SIT BACK (non-cryptic)
9. NAVAJO: N(JAVA reversed)O
9. SLEUTH (non-cryptic)
10. TEASE: [a]T EASE
10. ALLEN (non-cryptic)
12. GOBI: G[et] O[n] B[oats] I[magine]
12. OHMS (non-cryptic)
13. MEAT: ME (= "I object") + AT
13. DARK (non-cryptic)
15. FUTON (non-cryptic)
15. DENSE: NEEDS anagram
17. ERIC (non-cryptic)
17. KEEN: double definition
18. URGES (non-cryptic)
18. EAT-IN: [s]EATIN[g]
19. UPWELLS: U(POWELL - O)S
19. PRELACY (non-cryptic)
21. AFFIRM: hAlF oF dIgRaM
21. EITHER (non-cryptic)
25. CASTOR (non-cryptic); POLLUX: POLL + U[nicorn] + [o]X
26. JEKYLL (non-cryptic); MR HYDE: DR MY HE anagram
28. LESSON: LESSEN homophone
28. GARNER (non-cryptic)
31. RASPIER: PARRIES anagram
31. AUGMENT (non-cryptic)
33. FLOUT: F + LOUT
33. SEMIS (non-cryptic)
34. DUCK: D + U + C[as]K
34. WEED (non-cryptic)
35. MYRRH: MYRRH[a]
35. BEETS (non-cryptic)
36. LAOS: SO[k]AL reversed
36. COAX (non-cryptic)
37. OUZO: [bay]OU ZO[rba]
37. ODEA (non-cryptic)
39. ENSUE (non-cryptic)
39. STRUT: TRUST anagram
40. BINARY: B[ach] I[nvention] + NARY
40. HELIOS (non-cryptic)
41. INGENUE: ING(UNE reversed)E
41. BESMEAR (non-cryptic)
42. ERNST (non-cryptic)
42. CREPE: PEREC anagram
DOWN
1. ENG (non-cryptic)
1. COO: double definition
2. ALMAGEST: AL(MAGES)T
2. BABY TALK (non-cryptic)
3. WAXEN (non-cryptic)
3. GURUS: G(UR)US[h]
4. STITCH: [mo]ST ITCH[y]
4. DJINNI (non-cryptic)
5. THAN: [e]THAN
5. THEE (non-cryptic)
6. BARGEMEN: BAR + GEM + [frostbitt]EN
6. STAR WARS (non-cryptic)
7. NAVEL (non-cryptic)
7. CLARA: ARAL + C (= "Sea transcribed") reversed
8. UNICYCLIST: UN-ICY + C-LIST
8. MEANS TESTS (non-cryptic)
9. SHIRR: [eel]S [cuttlefis]H [ah]I [unde]R [heate]R
9. NOMAR (non-cryptic)
11. EVICT: T(CIV)E reversed
11. SMELT (non-cryptic)
14. PUBCRAWLER: BRAWL CUP anagram + [th]E [bende]R
14. LEOPARDESS (non-cryptic)
16. OPERATE: OPERA + T[h]E; SURGERY (non-cryptic)
20. ECHO (non-cryptic)
20. LIKE: LI(K)E
22. FLOP (non-cryptic)
22. ITEM: [exc]ITEM[ent]
23. FUMIGATE (non-cryptic)
23. TONE POEM: MONET anagram containing POE: TONE(POE)M
24. CYNOSURE (non-cryptic)
25. MYRMIDON: IN MY DORM anagram
27. JAUNT (non-cryptic)
27. QUEEN: QUE + [peopl]E + N[otice]
29. REEFER: [ca]REFREE anagram
29. SORTIE (non-cryptic)
30. FIXES: F(IX)ES
30. FUZZY (non-cryptic)
32. SCORN (non-cryptic)
32. GEESE: G[o] + E + ESE ("a couple of directions")
33. FRANC (non-cryptic)
33. STYLE: STY(L)E
35. BASE: double definition
35. MOON (non-cryptic)
38. ACT: CAT[s] anagram
38. ONE (non-cryptic)
The completed grids look like the following:
(non-cryptic down, cryptic across:)
(cryptic down, non-cryptic across)
2006 MIT Mystery Hunt