The friendly cryptic where nobody has to die!

Question

Warning: This puzzle may contain spoilers about Undertale and its plot. Please don't proceed if you don't want to be spoiled, since nothing will be in hide tags!

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Undertale was released for the Switch this year, and Deltarune was released recently too! This puzzle will revisit the Undertale universe, with all of its zany characters and morally challenging plot routes—as we know, there's three general routes you can take in Undertale: the Pacifist Route, the Genocide Route, and the Neutral Route. Each of the clues in this puzzle has chosen to follow exactly one of those routes, but when I played the game, it seems I didn't have much of a choice.

(1) The 20 clues on the Pacifist Route have each made friends with an Undertale character, with 4 clues for each of the 5 characters. For each of these clues, taking the n-th letter from the front of the clue, where n is the number associated with the character below, will tell you why I couldn't follow these clues along the Pacifist Route.

1. Toriel thinks that cryptic clues are too hard, so she's added an extra definition to each of them to try to hint them better.

2. Papyrus: NYEH-HEH-HEH!! I'VE TURNED ALL MY ENTRIES BLUE!!

3. Undyne's been throwing her spears in all directions, especially unconventional ones, and she might have thrown some entries too.

4. Alphys, as addicted to social media as always, can only find the time to transmit the clues over the phone.

5. Asgore still feels bad about the time he broke the SPARE button, so he's added SPARE letters to one word in each of his clues. They might have gotten a bit messy in the process, though.

(2) Instead, I followed the Genocide Route, along with 21 clues: each of them has had a visit from Sans, who's up to his practical jokes, as always. Each clue's wordplay half produces a string that is one letter longer than what its definition half defines (and that may or may not be a word). The word defined by the definition half, which should be entered, is thus this string, sans a character (ha!). Taking these extra characters, in clue order, will tell you the equally bad line I delivered once I defeated Sans.

(3) Finally, the remaining 17 clues in the puzzle followed the Neutral Route. They function as normal clues.

(4) Undertale is all about exploring where the line between right and wrong or good and evil lies, in order to find out what's truly important: thusly, highlight each cell on the grid which lies on the intersection between a Pacifist and Genocide entry. The highlighted letters, in clue order, will spell out the wordplay half of a final cryptic clue, which will show what's truly important in Undertale, depending on which route you've chosen!

Across
1 Servant's failure to gain river land
6 MBA, for example, hosts empty time for everyone (hyph.)
11 Current, fashionable model entering car
12 Attempt to take in love for wait system
13 Character with speech impediment to go back in time by infinitesimal amount
14 Magician Geller, formerly known as "Waste Material"
15 POOCH GROOVE appears in odd meta
17 Informally tell on in Australia home, heading out back
18 Recess time's right to follow clubs
20 Leading man journalist gazed at
22 Japanese hot spring's on mountain base, filled with brine
24 Professor with grand shadow
25 Selected column to showcase ancient architecture, ultimately
28 Ruins chocolate bar brand
30 Notes sea-scaper of legal importance
31 Employment of wise man after unemployment starts
35 Grants revolutionary sight to follow augur regularly
37 Sorcerers trap soldier
39 Establish group to chase thieves on the inside
40 Defeat—also, behead—soldiers from both sides
41 Mats rearranged to cover Regina's fly sting
42 Dynamic, pivotal role, but losing at club
45 In the middle of ammonia derivant
46 Thieves air gun, breaking into Sorre composition
47 "Plane": the composition's 23 by 28 inches
48 One in front of the other: time and—

Down
1 Vis-a-vis being eaten by leopards: man's fear
2 Hack advertising by the Ocean State
3 Spike drink with drugs, essentially, to be set up with thirst
4 Covered in gold—"shame!", we hear
5 Artist Schieren, of old Tokyo
6 Noble gas returning zero effects, briefly
7 Upset, primarily, engaged in cold complaint to duelist Aaron
8 Morale raised by excursions
9 Spaces containing negative ages
10 Color of flag on the radio
12 Crazy rant about Vietnamese dynasty
15 "Heartbreak! Paupers imprisoned by woman," Tom cries
16 "Introduction to Animation" to follow "Body Art Brief" later
17 British military award daring soldiers obtained, primarily (abbr.)
19 Outcomes of Erin neatly dusting staircases, from tops to bottoms
21 Wear clothing, heading out
22 Scored zero—it can be relied on (hyph.)
23 Blunt blades were sharp once, too; edge softens, in the end
24 Raffle to give away a, er, musical instrument
26 Currency related to nervous system
27 Plastered and drunk, initially, rush to welcome ship
29 That head covering!
32 A profit, once more
33 Belt brief dirge out
34 Prohibitionist carrying, initially, expensive champagne to wrap
36 Twitch's Spring Sale market starts
38 Working plan to support personae: 1,000 rounds
39 Auditor's pen is cause of sore eyes
40 Tag, with front scratched off, for first murder victim
41 Blue's Clues ending with commercial
43 In the spotlight: Psy's latest books
44 Before queen and her heart

Answer 1

Here is the filled grid:

Explanation of Pacifist transformations:

Toriel's clues include one wordplay portion, and two distinct definition portions, all for the same word.
Answers to Papyrus' clues can become 'blue' in some manner. Three times, the answers can be directly associated to 'red', and have 'blue' counterparts; the fourth entry has a related word that is synonymous with 'blue'.
Answers to Undyne's clues are entered in reverse in their slots.
Alphys' clues include one word that has been replaced by a homophone.
Asgore's clues include one word that has been anagrammed with the additional letters {S,P,A,R,E}.

Clues, answers, and explanations:
ACROSS

1. Servant's failure to gain river land

This is a Genocide clue. The extra letter is T.
DRUDGE = servant; R [river] in DUD [failure], plus GET [land]

6. MBA, for example, hosts empty time for everyone (hyph.)

This is a Papyrus clue. "Blue" also means risque or obscene, so G-RATED becomes the entry X-RATED.
G-RATED = for everyone; T__E [empty time] in GRAD [MBA, for example]

11. Current, fashionable model entering car

This is a Genocide clue. The extra letter is H.
RIPTIDE = current; HIP [fashionable] and T [model, as in Ford Model T] inside RIDE [car]

12. Attempt to take in love for wait system

This is an Alphys clue. The word 'wait' should actually be 'weight' in the clue.
TROY = weight system; O [love, as in 0 in tennis] inside TRY [attempt]

13. Character with speech impediment to go back in time by infinitesimal amount

This is a Toriel clue.
EPSILON = character (Greek letter) AND infinitesimal amount (common variable in math for amounts that shrink to zero); LISP [speech impediment] reversed and inside [get back in] EON [time]

14. Magician Geller, formerly known as "Waste Material"

This is a Genocide clue. The extra letter is E.
URINE = waste material; URI [magician Geller] and NEE [formerly known as]

15. POOCH GROOVE appears in odd meta

This is a Genocide clue. The extra letter is R.
MUTT = pooch; RUT [groove] in M_T_ [odd (letters of) "meta"]

17. Informally tell on in Australia home, heading out back

This is a Genocide clue. The extra letter is E.
DOB = informally tell on, in Australia; ABODE [home] with no first letter A [heading out] and reversed [back]

19. Recess time's right to follow clubs

This is a Genocide clue. The extra letter is S.
APSE = recess; _E [time's right(most letter)] following SAPS [clubs]

20. Leading man journalist gazed at

This is an Undyne clue.
STARED = gazed at; STAR [leading man] plus ED. [journalist (editor)]

22. Japanese hot spring's on mountain base, filled with brine

This is a Genocide clue. The extra letter is A.
ONSEN = Japanese hot spring; ON [on] plus _N [mountain base (last letter)] containing SEA [brine]

24. Professor with grand shadow

This is a Genocide clue. The extra letter is N.
DOG = shadow, as in follow; DON [professor] plus G [grand]

25. Selected column to showcase ancient architecture, ultimately

This is a Genocide clue. The extra letter is E.
OPTED = selected; OP.ED. [column] containing _T _E [ancient architecture, ultimately (last letters)]

28. Ruins chocolate bar brand

This is a Papyrus clue. MARS is the Red Planet, so the entry is the Blue Planet: EARTH.
MARS = ruins AND chocolate bar brand

30. Notes sea-scaper of legal importance

This is an Asgore clue. The word 'sea-scaper' should actually be 'case' in the clue.
RES = notes (as in do-re-mi) AND case of legal importance (Latin for thing, common in legal terminology)

31. Employment of wise man after unemployment starts

This is a Neutral clue.
USAGE = employment; SAGE [wise man] after U_ [unemployment start(ing letter)]

35. Grants revolutionary sight to follow augur regularly

This is a Neutral clue.
AGREES = grants; SEE backwards [revolutionary sight] after A_G_R [augur regularly (every other letter)]

37. Sorcerers trap soldier

This is a Genocide clue. The extra letter is W.
MAGI = sorcerers; MAW [trap, as in mouth] plus G.I. [soldier]

39. Establish group to chase thieves on the inside

This is a Toriel clue.
SET = establish AND group; found hidden inside "chaSE Thieves"

40. Defeat—also, behead—soldiers from both sides

This is a Genocide clue. The extra letter is S.
LOSS = defeat; _LSO [also, behead] and S_S [soldiers from both sides (first and last letters)]

41. Mats rearranged to cover Regina's fly sting

This is a Toriel clue.
SMART = fly (as in fashionable) AND sting (as in ache); SMAT* [mats rearranged] containing R [Regina]

42. Dynamic, pivotal role, but losing at club

This is a Papyrus clue. Liverpool F.C. is nicknamed 'The Reds', so the entry is the club nicknamed 'The Blues', which is CHELSEA.
LIVERPOOL = club, as in football; LIVERPOOLAT* [dynamic (anagram) "pivotal role"] without the AT [losing at]

45. In the middle of ammonia derivant

This is a Genocide clue. The extra letter is E.
AMID = in the middle of; AMIDE [ammonia derivant]

46. Thieves air gun, breaking into Sorre composition

This is a Neutral clue.
ROBBERS = thieves; BB [air gun] inside ROERS* ["sorre" composition (anagram)]

47. "Plane": the composition's 23 by 28 inches

This is a Papyrus clue. The elephant is the mascot animal for the Republicans (Red) in the USA, so the entry is the mascot animal for the Democrats (Blue) in the USA, which is the DONKEY.
ELEPHANT = 23 by 28 inches, as a sheet size; ELEPHANT* ["plane the" composition (anagram)]

48. One in front of the other: time and—

This is a Neutral clue.
TANDEM = one in front of the other; T [time] plus AND [and] plus EM [— (a typographic unit of length)]

DOWN

1. Vis-a-vis being eaten by leopards: man's fear

This is an Asgore clue. The word 'leopards' should actually be 'old' in the clue.
DREAD = fear; RE: [vis-a-vis] inside DAD [old man]

2. Hack advertising by the Ocean State

This is a Genocide clue. The extra letter is R.
RIP = hack; P.R. [advertising] after R.I. [Ocean State]

3. Spike drink with drugs, essentially, to be set up with thirst

This is a Genocide clue. The extra letter is I.
UPSURGE = spike; SIP [drink] plus U [drugs, essentially (central letter)], reversed [set up], plus URGE [thirst]

4. Covered in gold—"shame!", we hear

This is a Neutral clue.
GILT = covered in gold; homophone [we hear] of GUILT [shame]

5. Artist Schieren, of old Tokyo

This is an Alphys clue. The word "Schieren" should actually be "Sheeran" in the clue.
EDO = (old) Tokyo; ED [artist Sheeran] plus O [old]

6. Noble gas returning zero effects, briefly

This is a Genocide clue. The extra letter is F.
XENON = noble gas; NONE FX [zero effects, briefly] reversed [returning]

7. Upset, primarily, engaged in cold complaint to duelist Aaron

This is an Undyne clue.
BURR = duelist Aaron; U_ [upset, primarily (first letter)] in BRR [cold complaint]

8. Morale raised by excursions

This is a Genocide clue. The extra letter is I.
TRIPS = excursions; reversal [raised] of SPIRIT [morale]

9. Spaces containing negative ages

This is a Genocide clue. The extra letter is N.
EONS = ages; ENS [spaces (typographic)] containing NO [negative]

10. Color of flag on the radio

This is a Neutral clue.
DYE = color; homophone [on the radio] of DIE [flag, as in decline/fade]

12. Crazy rant about Vietnamese dynasty

This is a Neutral clue.
TRAN = Vietnamese dynasty; TRAN* [crazy (anagram) "rant"]

15. "Heartbreak! Paupers imprisoned by woman," Tom cries

This is an Asgore clue. The word 'Paupers' should actually be 'up' in the clue.
MEOWS = Tom (as in male cat) cries; WOE [heartbreak] reversed [up] inside MS. [woman]

16. "Introduction to Animation" to follow "Body Art Brief" later

This is a Neutral clue.
TA-TA = brief "Later!"; A_ [introduction (first letter) to animation] following TAT [body art]

17. British military award daring soldiers obtained, primarily (abbr.)

This is a Neutral clue.
DSO = British military award (Distinguished Service Order); initials [primarily] of "daring soldiers obtained"

19. Outcomes of Erin neatly dusting staircases, from tops to bottoms

This is a Toriel clue.
ENDS = outcomes AND bottoms; initials [tops] of "Erin neatly dusting staircases"

21. Wear clothing, heading out

This is a Genocide clue. The extra letter is T.
TIRE = wear; ATTIRE [clothing] without the first letter A [heading out]

22. Scored zero—it can be relied on (hyph.)

This is an Undyne clue.
GO-TO = it can be relied on; GOT 0 [scored zero]

23. Blunt blades were sharp once, too; edge softens, in the end

This is a Genocide clue. The extra letter is O.
EPEES = blunt blades; final letters [in the end] of "were sharp once too edge softens"

24. Raffle to give away a, er, musical instrument

This is a Genocide clue. The extra letter is W.
DRUM = musical instrument; DRAW [raffle] without the A [give away a], plus UM [er (hesitation)]

26. Currency related to nervous system

This is a Genocide clue. The extra letter is N.
EURO = currency; NEURO [related to nervous system]

27. Plastered and drunk, initially, rush to welcome ship

This is a Neutral clue.
DRESSED = plastered; D_ [drunk, initially], plus REED [rush (plant)] containing S.S. [ship]

29. That head covering!

This is a Neutral clue.
HAT = head covering &lit. (the entire clue is both definition and wordplay); the first letter [head] of "that" covers the remaining part "hat"

32. A profit, once more

This is a Neutral clue.
AGAIN = once more; A GAIN [a profit]

33. Belt brief dirge out

This is a Neutral clue.
GIRD = belt; DIRG_ [brief (all but last letter) dirge] anagrammed [out]

34. Prohibitionist carrying, initially, expensive champagne to wrap

This is an Alphys clue. The word 'wrap' should actually be 'rap' in the clue.
DECRY = rap; DRY [prohibitionist] containing E_ C_ [initially, expensive champagne]

36. Twitch's Spring Sale market starts

This is a Neutral clue.
SPASM = twitch; SPA [(hot) spring] plus S_ M_ ["sale market" starts]

38. Working plan to support personae: 1,000 rounds

This is an Asgore clue. The word 'personae' should actually be 'one' in the clue.
AMMO = rounds; M.O. [working plan] following A [one] plus M [1,000]

39. Auditor's pen is cause of sore eyes

This is a Neutral clue.
STYE = cause of sore eyes; homophone [auditor's] of STY [pen]

40. Tag, with front scratched off, for first murder victim

This is an Undyne clue.
ABEL = first murder victim; LABEL [tag] with no first letter L [front scratched off]

41. Blue's Clues ending with commercial

This is a Neutral clue.
SAD = blue; _S ["clues" ending] plus AD [commercial]

43. In the spotlight: Psy's latest books

This is an Alphys clue. The word 'Psy' should actually be 'sigh' in the clue.
HOT = in the spotlight; _H ["sigh"s latest (last letter)] plus OT [books (Old Testament)]

44. Before queen and her heart

This is a Neutral clue.
ERE = before; ER [queen (Elizabeth, Regina)] plus E ["her" heart (central letter)]

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Why Couldn't I Follow The Pacifist Route:

BECAUSE MY LV IS TOO HIGH
Explaining this one gets more spoiler-y into Undertale than I wish. But, yeah, Level 51 is way too high.

Post-Sans One Liner:

THERE'S A NEW SERIF IN TOWN
Sans (and Papyrus) are named for typefaces (which they aptly use in their text boxes). Specifically, Sans is named for Comic Sans / Comic Sans Serif.

Exploring What's Truly Important:

The intersection letters spell "DEXTER DROPS NUMBER TO NOTE REALM".
This is wordplay for: DEXTER minus the X [drops number (X=10)], plus MI [note] plus NATION [realm].
So what truly important is DETERMINATION, which is definitely an important concept in Undertale.

Exploring What's Truly Important (REDUX):

Level 51 indicated a second part to this clue.
The intersection letters spell "DEXTER DROPS NUMBER TO NOTE REALM".
This is wordplay for: DEXTER minus the D [drops number (D=500)], plus MI [note] plus NATION [realm].
So what truly important is EXTERMINATION, which is definitely an important concept in Undertale, especially to the sort of person who would go on a Genocide run and use file-editing to reach Level 51 when the actual levels only go up to 20!
(ꐦ ಠ皿ಠ )

Answer 2

Grid:

Solutions, classifications, words needed to make sense of Papyrus and Asgore clues, and letters obtained from Pacifist and Genocide clues:

Across 1 DRUDGE Genocide T 6 X-RATED Pacifist Papyrus B G-RATED 11 RIPTIDE Genocide H 12 TROY Pacifist Alphys E WEIGHT 13 EPSILON Pacifist Toriel C 14 URINE Genocide E 15 MUTT Genocide R 17 DOB Genocide E <-- I don't actually understand this one 18 APSE Genocide S 20 STARED Pacifist Undyne A 22 ONSEN Genocide A 24 DOG Genocide N 25 OPTED Genocide E 28 EARTH Pacifist Papyrus U MARS 30 RES Pacifist Asgore S 31 USAGE Neutral 35 AGREES Neutral 37 MAGI Genocide W 39 SET Pacifist Toriel E 40 LOSS Genocide S 41 SMART Pacifist Toriel M 42 CHELSEA Pacifist Papyrus Y LIVERPOOL 45 AMID Genocide E 46 ROBBERS Neutral 47 DONKEY Pacifist Papyrus L ELEPHANT 48 TANDEM Neutral Down 1 DREAD Pacifist Asgore V OLD 2 RIP Genocide R 3 UPSURGE Genocide I 4 GILT Neutral 5 EDO Pacifist Alphys I SHEERAN 6 XENON Genocide F 7 BURR Pacifist Undyne S 8 TRIPS Genocide I 9 EONS Genocide N 10 DYE Neutral 12 TRAN Neutral 15 MEOWS Pacifist Asgore T UP 16 TATA Neutral 17 DSO Neutral 19 ENDS Pacifist Toriel O 21 TIRE Genocide T 22 GOTO Pacifist Undyne O 23 EPEES Genocide O 24 DRUM Genocide W 26 EURO Genocide N 27 DRESSED Neutral 29 HAT Neutral 32 AGAIN Neutral 33 GIRD Neutral 34 DECRY Pacifist Alphys H RAP 36 SPASM Neutral 38 AMMO Pacifist Asgore I ONE 39 STYE Neutral 40 ABEL Pacifist Undyne G 41 SAD Neutral 43 HOT Pacifist Alphys H SIGH 44 ERE Neutral

Extraction from Pacifist clues:

BECAUSE MY LV IS TOO HIGH (which I believe makes sense in the context of Undertale)

Extraction from Genocide clues:

THERE'S A NEW SERIF IN TOWN (which seems plausible; note that the guy's name is Sans)

Extraction from intersections of P and G clues:

DEXTER DROPS NUMBER TO NOTE REALM (which yields DETERMINATION)

[EDITED to add:]

There's a bit of extra subtlety in that last bit of wordplay, because there are two numbers you can drop from DEXTER. One way gets you DETERMINATION, and the other gets you EXTERMINATION. How very appropriate! (Credit where due: I didn't notice this for myself; MPH got it from an edit L51 made to the question after I posted the original version of this answer.)