Arc (&) Reactors

Question

(Note: This puzzle may require a small amount of research if you aren't familiar with the work from its theme.)

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It was exactly 11 years ago -- April 14, 2008, in Sydney -- that the first Iron Man movie premiered, featuring the power-generating "arc reactor". But here, we'll be looking at different arcs and reactors.

(1) A certain period of time in the past, an arc began in a work of fiction. This arc parallels a very similar one that will occur that same period of time in the future. Nine clues and answers are completely normal; the clues' first letters spell out the period of time, and their last letters spell out the work of fiction in question.

(2) Eleven characters from said work are 'reacting' to the arc, each changing one answer during entry in a characteristic way. (Two of the new entries do not have "dictionary nature"; one is a two-word abbreviation, and the other is a specialized term.) Because of these changes, the grid makes several distinctions that are not normally made, and some cells' contents are unusual. The character changing each answer is associated with one element of a repeating sequence. For the character associated with the nth element, take the nth letter from both the start and end of the clue. These letters will spell out a description of the outcome of the past arc (which is strikingly similar to the future arc).

(3) To aid in finding these changes, eleven other clues have an extra sequence of one or more words that must be removed before solving. These sequences define the altered entries from (2) (though not in order).

It may seem that one character is missing from the 11 reacting characters from (2). The starts of each of these definitions, again in clue order, will spell out the seemingly missing character (in an appropriate way).

(4) The remaining 28 clues all have a single incorrect letter, which must be changed to another letter for the clue to be solved. These changes may not preserve the surface meaning of the clue.

The incorrect letters of both Across and Down clues will spell out a short plot summary of the events just before the first arc (which also happens to be a cryptic clue for the object involved in the second arc).

That twelfth character has made themselves known in the correct letters of the Across clues, which will form a descriptive phrase that applies three times to parts of this puzzle. These point to appropriate words describing how the two arcs are related, how they might know that, and what the arcs might lead to.

And finally, the correct letters of the Down clues will briefly describe the arc in the future (giving the solution to the aforementioned clue, as well as a detail that explains why some of those words -- and the initial reaction to that arc -- aren't as accurate as they seem).

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Across
1. English energy drink made from cola, due to be mixed with a bit of zest
7. Sports equipment, start to finish, was a sign of affection
10. Don't have a Kia: design secretes a horrible smell
12. Otter kin heard by flirtatious woman
14. "Claimant dusted me", man recalled, "with powder"
17. One leaning, honest fabulist in speech
18. Units of sound intensity initially described by Socrates
19. Nobleman Lear in rain
20. Verse in modern song by Zayn Malik
21. Appropriately crazy dare by Plato
24. Vulgar overcomplicator's advice is primarily contrived and impolite
25. Holiday local to Glasgow when Trotsky is overthrown
26. Sands a moon shape after scratching coin
27. Beer ingredient found in optimal-temperature lager, maybe
29. Need a tattletale's secret info
31. Poor quality, terrible roll of a 2
33. Setter Reagle's coat pattern is chased too soon
34. Wind cools turnover
36. Author's unsuccessful score with hot mate
37. Essentially, Gotti is the champion for Minnesota team
38. Massachusetts city camels ill-prepared to ditch element of uranium
39. Barres's position in an idiom is taking up space, capturing resistance
42. Unknown big cipher with actress Felicia
43. Burial site of Homer obscured by radio silence
46. Circle naves of Linda with much outcry
47. Vocal Kelly the astronaut's retribution
48. Bet xanthic cat ate entertaining knight
49. Big assembly from hosting pair of events
50. Duplicated author's viral joke
51. East Indian state donkey having identical outbreak of elephantiasis

Down
1. In pairs, complain about praise
2. So, cadet fixed rag without effort
3. Alternatively, halt author
4. In the morning, Erich makes a patrotic ballad
5. Baaing odd filly might lead you to herb
6. Conversationally persuaded each mean motorcyclist delinquent
8. Character with entity for Othello and one in the past
9. Dirtbed deals for Teen Titans villain
11. Scrap of oat removed from homeless animal's plate
13. Relative is kind when assuming romance's cloying
14. Agony of trolley car #1 beset with extreme snafu
15. A conman's located, surrounded by shrieking
16. Diminish threes, dropping first half for singer Juice
22. Annoy king needing writer
23. Drow has right item from quiver
25. Book with karaoke selections
28. Drop characters written in Michelangelo's epic
30. Touch Apple product and a Kindle
31. Triply scolded babies
32. Think second-class Biblical woman would take leaf
35. Tech wizard's sons I improperly treated?
36. Police drama might trim down chaos
37. Strap for horse side or hair
38. Erstwhile car company's sheepish remarks making a comeback
40. Fate of Pompeii's entrance without tall man
41. Maneuver through 2-somes of pyramids, poisonous gas, and weaponry
42. Overturned request politician secretly votes for
44. Announced baseman Sadaharu also is gay
45. Island runner's goal (when aiming low) is celestial energy

Answer 1

Here, first of all, is the grid.

(1) an arc began in a work of fiction... Nine clues and answers are completely normal; the clues' first letters spell out the period of time, and their last letters spell out the work of fiction in question.

The work of fiction is Andrew Hussie's HOMESTUCK. The period of time is ONE DECADE. The earlier arc is the first of the story in 2029, in which one character plays a computer game that somehow causes the earth to be struck by meteors and destroyed. The later is in 2029 -- I'm not sure whether it has anything to do with the story, because this is a thing in real life -- when the asteroid Apophis will come fairly close to the earth. (Perhaps the "arc" second time around is the orbital path of Apophis rather than a story arc?)

O H relier       17a One leaning, honest fabulist in speech
N O data         29a Need a tattletale's secret info
E M twins        37a Essentially, Gotti is the champion for Minnesota team
D E meme         50a Duplicated author's viral joke
E S Assamese     51a East Indian state donkey having identical outbreak of elephantiasis
C T 1%er          6d Conversationally persuaded each mean motorcyclist delinquent
A U trauma       14d Agony of trolley car #1 beset with extreme snafu
D C lose         28d Drop characters written in Michelangelo's epic
E K Saab         38d Erstwhile car company's sheepish remarks making a comeback

Notes: 17a. REAL LIAR. 29a. neeDATAttletale's. 37a. goTti + WINS. 50a. ME+ME. 51a. AS(SAME)S+E. 6d. "Won per centre"; I'm not familiar with the definition but will take Deusovi's word for it :-). 14d. TRAM A containing (snaf-)U. 28d. michelangeLOSEpic. 38d. BAAS<.

(2) Eleven characters from said work

Eleven of the twelve "internet trolls". (The odd one out is Sollux.)

changing one answer during entry in a characteristic way

They all have distinctive typing quirks.

the grid makes several distinctions that are not normally made, and some cells' contents are unusual

Capital and lowercase letters both appear, and the difference matters; we also have digits and other characters.

associated with one element of a repeating sequence

The signs of the zodiac.

For the character associated with the nth element, take the nth letter from both the start and end of the clue. These letters will spell out a description of the outcome of the past arc (which is strikingly similar to the future arc).

Here we go:

E A lUcOzAdE     Gamzee 10  1a English energy drink made from cola, due to be mixed with a bit of zest
R T KISS         Karkat  4  7a Sports equipment, start to finish, was a sign of affection
H I min%         Equius  9 12a Otter kin heard by flirtatious woman
S S d8s          Vriska  8 18a Units of sound intensity initially described by Socrates
T R crab         Feferi 12 31a Poor quality, terrible roll of a 2
U C iOS          Tavros  2 43a Burial site of Homer obscured by radio silence
K B Scot         Kanaya  6 47a Vocal Kelly the astronaut's retribution
Y A bevvy        Eridan 11 49a Big assembly from hosting pair of events
M E cheetah      Nepeta  5 15d A conman's located, surrounded by shrieking
T E NUMB3RS      Terezi  7 25d Book with karaoke selections
O R 0pts         Ariada  1 42d Overturned request politician secretly votes for

So we read: EARTH IS STRUCK BY A METEOR. ("Strikingly similar", ho ho.)
The numbers in column 5 are zodiac sign numbers starting with Aries. Notes: 1a. (COLA DUE Z)*. 7a. SKIS. 12a. MINX. 18a. dBs. 31a. CRAP; Feferi is making a fish pun, kinda. 47a. Scott Kelly; "scot-free". 49a. EV(ents) in BY, V doubled by Eridan. 15d. AT inside CHEER making CHEATER; Nepeta likes cat puns. (Also tends to turn EE into 33, but apparently not here; OP confirms that this is an oversight, though it seems a very reasonable one since 33ifying spoils the cat pun a little.) 25d. Double def. 42d. Backwards in requeSTPOlitician.

(3) eleven other clues have an extra sequence of one or more words [...] define the altered entries from (2). [...] The starts of these definitions [...] will spell out the seemingly missing character

Here are the clues and their answers, with angle brackets around the extra words.

ode     lUcOzAdE 20a Verse in modern <song by Zayn Malik>
crude   KISS     24a Vulgar <overcomplicator's advice> is primarily contrived and impolite
Noel    Scot     25a Holiday <local to Glasgow> when Trotsky is overthrown
malt    bevvy    27a Beer ingredient found in optimal-temperature <lager, maybe>
mesh    0 pts    36a Author's <unsuccessful score> with hot mate
ante    cheetah  48a Bet <xanthic cat> ate entertaining knight
laud    crab      1d In pairs, <complain> about praise
alight  iOS      30d Touch <Apple product> and a Kindle
mayhem  NUMB3RS  36d <Police drama> might trim down chaos
coax    d8s      41d Maneuver through <2-somes of pyramids>, poisonous gas, and weaponry
Skye    min %    45d Island <runner's goal (when aiming low)> is celestial energy

Second column indicates the thing being defined.
The definitions' first letters spell out SOLLUXCAP2R. Sollux's full name is SOLLUX CAPTOR and we're quirkily replacing TO with 2 (I think that's a thing Sollux does). So, Sollux is the missing troll.
Notes: 20a. mODErn. 24a. C+RUDE. 25a. LEON<. 27a. optiMALTemperature. 36a. ME'S+H. 48a. N in ATE. 1d. DUAL<. 30d. A LIGHT. 36d. MAY HEM. 41d. CO+AX. 45d. SKY E.

(4) a single incorrect letter [...] incorrect letters of both [...] will spell out a short plot summary [...] which also happens to be a cryptic clue for the object involved in the second arc. [...] That twelfth character has made themselves known in the correct letters of the Across clues, which will form a descriptive phrase that applies three times to parts of this puzzle. These point to appropriate words describing how the two arcs are related, how they might know that, and what the arcs might lead to. [...] the correct letters of the Down clues will briefly describe the arc in the future [...] as well as a detail that explains why some of those words -- and the initial reaction to that arc -- aren't as accurate as they seem

OK, this is where I get into some difficulties, because I haven't solved all the clues and a few things don't make sense. (Perhaps I have misidentified one or more clues above too?) Anyway, here first of all are the clues and (so far as I know them) the letter corrections and answers. Corrections are listed in columns and also indicated in the clues.

A D abort        10a Don't have a Ki(a->d): design secretes a horrible smell
D O talc         14a "Claimant (d->o)usted me", man recalled, "with powder"
A U earl         19a Nobleman Lear in r(a->u)in
D B aptly        21a Appropriately crazy (d->b)are by Plato
S L acres        26a (S->L)ands a moon shape after scratching coin
H E Merl         33a Setter Reagle's coat pattern is c(h->e)ased too soon
O I spool        34a Wind coils turnover
U C Salem        38a Massachusetts city camels ill-prepared to ditch element of (u->c)ranium
S L 3rd          39a Barre(s->l)'s position in an idiom is taking up space, capturing resistance
I U 0day         42a Unknown b(i->u)g cipher with actress Felicia
N E hoopla       46a Circle (n->e)aves of Linda with much outcry
G N coasted       2d So, cadet fixed ra(g->n) without effort
T E Orwell        3d Alternatively, hal(t->e) author
H A America       4d In the morning, Eric(h->a) makes a patrotic ballad
A R dill          5d Ba(a->r)ing odd filly might lead you to herb
T M Iago          8d Character with en(t->m)ity for Othello and one in the past
B I Slade         9d Dirt(b->i)ed deals for Teen Titans villain
O S tray         11d Scrap of (o->s)at removed from homeless animal's plate
Y S niece        13d Relative is kind when assuming romance's clo(y->s)ing
E O v8           16d Diminish thr(e->o)es, dropping first half for singer Juice
N F poke         22d Annoy king (n->f)eeding writer
D A arrow        23d (D->A)row has right item from quiver
L P coddles      31d Trip(l->p)y scolded babies
E O believe      32d Think second-class Biblical woman would take l(e->o)af
S P psion        35d Tech wizard's (s->p)ons I improperly treated?
S H trace        37d Strap for horse (s->h)ide or hair
L I doom         40d Fate of Pompeii's entrance without ta(l->i)l man
Y S O2           44d Announced baseman Sadaharu also is ga(y->s)

So the incorrect letters spell out: A DAD'S HOUSING THAT BOY ENDLESSLY. I don't know anything much about Homestuck, but the title suggests that this might fit well enough.
The corrected Across letters spell out: DOUBLE I CLUE. There are exactly three of these, counting "I <space> I" as a double-I: 37a (TWINS), 35d (PSION), 40d (DOOM). I take it that means that the arcs are TWINS; "they" know by applying PSIONic powers; and the meteor/asteroid strikes could bring DOOM.
The corrected Down letters spell out: NEAR MISS OF APOPHIS. That at least is straightforward enough.
The cryptic clue is also straightforward enough: A POP'S contains HI(m).
I suppose the "detail" (which personally I would consider much more than a detail) is the fact that Apophis is going to miss the earth, rather than hitting it as in Homestuck, so the arcs aren't quite TWINS after all and the earth isn't DOOMed just yet). Notes: 10a. BO in ART. 14a. CLA(iman)T<. 19a. LEAR*. 21a. *(b)YPLAT(o))*. 26a. A CRES(cent). 33a. MERL(e); Merl Reagle. 34a. LOOPS<. ("Wind", verb.) 38a. (c)AMELS*. 39a. Lock, stock, and ... 42a. 0=cipher. Felicia Day. 46a. HOOP+L(ind)A. 2d. (SO CADET)*. 3d. OR WELL. 4d. AM ERICA. 5d. (o)D(d) (f)ILL(y). 8d. I AGO (the I is a Roman numeral, not the result of trollish quirkery). 9d. DEALS*. 11d. (s)TRAY. 13d. E in NICE. 16d. ALLEVIATE minus first half of the syllables ("for singer"); not sure what indicates VIATE->V8; not sure whether V should be capital or lowercase (usual default is lowercase but the juice capitalizes it). 22d. K in POE. 23d. R in AROW. 31d. SCOLDED*. Babies, verb. 32d. LIE in B EVE. 35d. (PONS I)*. 37d. Double definition. 40d. DOO(r)+M. 44d. Homophone of "OH TOO".

Credit where due:

Thanks to @ffao for explaining how the wordplay for 16d might work. My explanation above is a slight modification of his; OP confirms that it's what's intended. And thanks also to @ffao for suggesting considering double letters across spaces, which I'm not sure I'd ever have thought of. (Having clearly figured out the correct analysis of 34a, which at that point I hadn't.) Thanks to @Deusovi for pointing out some minor errors when all ways done; I have now adjusted them above.