This is actually fairly common. Weird events often occur during an adventurer's adventures, and sometimes an adventurer gains permanent powers from those weird events. In other words,
Yes, There's Precedent
- In Advanced Dungeons and Dragons DMs were sort of expected to run adventures that changed characters--usually for ill. The Dungeon Master's Guide (1978) has Appendix H: Tricks (216-7), which describes an altar that can "age the character 10 years," an arch that can change a character's sex; and a pedestal that can "lower one attribute of the character by 1 point" or "turn the character permanently invisible." While none of these are particularly attractive, all are permanent changes gained via an adventuring.
Also in Advanced Dungeons and Dragons, magic items--which were not supposed to be purchased (despite having gp values), sparsely available, and rarely manufactured--were mysterious, and experimentation with them could lead to increased character power. Perhaps the most famous example was the Potion Miscibility Table.
Potions in AD&D were like any other magic items--and, potentially, just as lethal. A creature who drank a second potion while under the influence of a first (or a fool who, like, gulped two a potions at once) rolled on the Potion Miscibility Table (119), which could cause the combined potions to explode inside the drinker, to create a poison in the drinker's belly, or to function maybe a little better or worse than normal... or to give the character a super power, a discovery that causes one of the drunk potion's effects to become permanent. Considering possible AD&D potions included potions of dragon-control, invulnerability, speed, and treasure finding, this could let a character win AD&D... except the DM determined the exact effects of the discovery and was likely to bone the character anyway.
Wizards of the Coast published a Potion Miscibility Table for Dungeons and Dragons 3.5 in the article "'I Wouldn't Drink That If I Were You': Potion Miscibility."
In addition, until Dungeons and Dragons, 4th Edition (and maybe even then--it's not my thing) all versions of Dungeons and Dragons made artifacts a a possible way to permanent power or misfortune. From the deck of many things in the Dungeon Master's Guide (1978) for Advanced Dungeons and Dragons, to an artifact's curse that "cause[s] the user's touch to have a 50% chance of draining the magic from any item not an artifact" (10) from the Encyclopedia Magica Vol. 1 for Advanced Dungeons and Dragons, 2nd Edition to the great elixir (57-8) in Shining South for Dungeons and Dragons, 3rd Edition, artifact interaction--regardless of character level--leading to vast power, despair, or both has been a thing.
Dungeons and Dragons 3.5 produced teamwork benefits in Dungeon Master’s Guide 2, Dungeonscape, Forge of War, Heroes of Battle, and Player’s Handbook 2. Although a "team must have at least two members," it only takes an Intelligence score of 3 to be part of a team, so while most druid's animal companions won't qualify, a special mount a la the paladin and a familiar a la the wizard, the sorcerer, and the feat Obtain Familiar (CAr 81) certainly does. Teamwork benefits are limited to 1 per 4 levels or HD, but the cost is minimal--the team leader must have a few skill ranks or a feat or two (usually which he already had), each team member needs to meet far less stringent yet still present prerequisites, and the team must spend 2 weeks training and periodically meetup to train to keep the benefit.
Teamwork benefits are tiny, though. For example, the teamwork benefit Climbing Squad (Du 47) allows the team leader to grant team members a +4 bonus to Climb skill checks when the team leader uses the aid another action to help team members climb something he's currently summited.
Also for Dungeons and Dragons 3.5 Wizards of Coast published a variety of magical locations and legendary sites (CS 143-52). Unlike planar touchstones (PlH 153-86) or touchstone sites (Sa 54-64) which require the feat Planar Touchstone (PlH 41-2) and the feat Touchstone (Sa 53), respectively, magical locations have no feat requirement. They do, however, usually require characters who want to gain their benefits to perform some act, meet prerequisites, or both, before the power's gained. These benefits vary significantly.
The most famous of legendary sites is Otyugh Hole (CS 152-3), a filthy solitary prison cell in which a character can spend a week to get his choice of 1 feat from a short list that includes the feat Iron Will (PH 97); the book prices this event at 3,000 gp.
I don't think that this means the character is supposed to just pay some weirdo 60 lbs. of gold for the right to sleep in a septic tank for a week and emerge with the feat Iron Will.1 It's supposed to be an adventure. The character gets thrown into the septic tank for a week, suffers, goes hungry, is almost driven mad, writes his name on the wall with his own feces, and is rescued by someone to whom he now owes something... or whatever. The reason it has a value is because it permanently adds something to the character, and that comes at a cost. According to Complete Scoundrel a legendary location, like a magical location, has an Ability Value entry because
Although these abilities can never be bought or sold, they can be substituted for treasure of like value and count toward the benefiting character’s overall wealth. (142)
The game expects characters to expend a resource for increased power. In the case of abilities granted by touchstones, that's a feat. In the case of legendary sites and magical locations, that's treasure.
Finally, for Dungeons and Dragons 3.5 there are affiliations (City of Stormreach 91-121, CC 6-44, DM 141-6, DrU 23, Du 57-62, PH2 163, and the formerly-hosted-by-the-Wizards-of-the-Coast-Web-site-but-now-removed article "The Allure of Evil: Dark Churches"). Unlike legendary sites and magical locations, affiliations have no cost, but, like them, affiliations often have prerequisites that must be met before membership's approved and advancement in the ranks is usually accomplished via performing tasks on the affiliation's behalf.
Low-ranking affiliation benefits are often nonexistent or inconsequential, while high-ranking benefits are often worthy of their significant investment for the right character (e.g. the highest ranked members of Fharlanghn’s Way (CC 14-15) can, 1/day for 1 round/3 levels, use a spell-like ability to become ethereal; the highest ranked Fingers of the Laughing Rogue (CC 15-16) can, 1/day, force a foe to reroll an attack, check, or saving throw after the result's known).
Standards for Granting Unique Abilities
Thus are established several different standards for granting a character unique abilities. You can pick one, several, or all.
When the plot demands it. This is easiest, and the Gygaxian adventure standard. There are things in the campaign that exist only to alter adventurers.
For example, an arch exists that does random stuff. The character hears legends of the Arch of Unpredictability. If he finds it and passes through it, something random happens for good or ill--mostly ill. However, if the character has no method to mitigate the effects, this could lead to the campaign's end.
Alternately--and better for the game--is creating status quo or tailored encounters designed to grant the character the unique abilities that the player wants the character to have or that the character needs, whether immediately or in the future.
For example, if using the Potion Miscibility Table, you could rule that the first time the character chugs a pair of potions--by accident or design--the character gains a unique ability, but, thereafter, the character rolls.2
For example, if approaching a dragon's lair, the magic pond just beyond the dragon's sphere of influence might grant a bather the ability to use 1/day as a spell-like ability an effect like the 3rd-level Sor/Wiz spell antidragon aura [abjur] (SpC 14), but the potential bather must convince the fey that guard it that he is worthy of the pond's power via surviving a dinner with them, solving their riddle, wrestling their grig champion, or vanquishing one of their lesser foes.
Upon attaining a new experience level. Even Wizards of the Coast acknowledged that levels in character classes that advance only by table (instead of also granting one or more new abilities) are boring. A pair of Character Class columns "Dead Levels: Character Class Companion" and "Dead Levels II: Character Class Companion" partially and in an only barely satisfactory method addresses this concern, but, seriously, if you're running a game for 1 PC and that PC levels up and gets only bigger numbers, you should totally step in and change that.
Upon gaining a feat because of attaining a new experience level. Thus grant the character a unique ability at levels 1, 3, 6, 9, 12, 15, and 18. Each level-up feat could have been the feat Planar Touchstone or Touchstone, and those can grant unique abilities. Use abilities the character could have gained via those feats as guidelines, looking particularly at lower-order abilities for guidance.
Upon attaining character level 4 or 4 Hit Dice and each 4 levels or Hit Dice thereafter. This is the standard established by teamwork benefits. A relatively small unique ability granted for training montages. This lets you reward the character for having sought out Hidden Masters of Secret TechniquesTM yet be able to justify it in game with mechanics. A solo game shouldn't punish a PC more for being alone, and his inability to gain teamwork benefits limits his power. Make up for these "lost" benefits with unique abilities.
When the character can afford it. This is the standard established by legendary sites and magical locations. Instead of granting raw cash or magic items as treasure, grant unique abilities.
For example, Table 3-3: Treasure Values per Encounter (DMG 51) lists a level 8 encounter's treasure value at 3,400 gp. As Complete Scoundrel prices Otyugh Hole's benefits at 3,000 gp, a character who spends a week in a filthy dungeon, fighting monsters and starving, could fight the final EL 8 boss, loot the boss's masterwork spiked chain and 25-gp gem, and find, upon emerging from the dungeon, that he now has the strength of will to soldier on despite horrifying adversity, gaining the feat Iron Will.
There are--if you squint and look sidelong--ways of pricing additional feats if you need guidelines for that. According to the sidebar Magic Items that Grant Feats in the Arms and Equipment Guide:
If a feat is purely mechanical, such as Great Fortitude, default to the rules in the Dungeon Master's Guide with an adjustment for the fact that the bonus has no type. For instance, the belt of endurance grants Great Fortitude, which adds a +2 bonus on all Fortitude saves. A +2 resistance bonus on all saves would cost 4,000 gp. It shouldn't be more or as economical to buy bonuses to all saves separately, so a +2 bonus on Fortitude saves alone should cost 2,000 gp. If the bonus has no type assigned to it, you could double or even triple that....
A general guideline for other kinds of feats is that they cost 10,000 gp, plus another
5,000 gp to 10,000 gp per prerequisite. (128)
Keep in mind that the Arms and Equipment Guide is on the cusp of the Dungeons and Dragons, 3rd Edition revision, and, while this advice does provide a guideline, the Magic Item Compendium and other Dungeons and Dragons 3.5 sources provide examples of cheaper, non-numeric feat-granting items (e.g. gloves of the balanced hand (MIC 105) (8,000 gp; 0 lbs.), which grant the wearer either the benefits of the feat Two-weapon Fighting (PH 102) or the benefits of the feat Improved Two-weapon Fighting (PH 96), but let their wearer ignore the Dexterity ability score prerequisite or the Dexterity ability score and Base Attack Bonus prerequisites, respectively). Remember to factor in that feats granted this way will be slotless items (i.e. the entry No space limitation on Table 7-33: Estimating Magic Item Gold Piece Values (DMG 285)).
Upon completing one or more important campaign-specific events. This is the standard set by affiliations. You can throw out the affiliation's need to actually associate with those folks and instead virtually advance the character's affiliation score based on the campaign's events.
For example, a character's affiliation score in the Brotherhood of Equals (CC 11-12) increases by 4 if the character "frees someone from captivity or slavery." Doing this once is sufficient to grant the character rank 1 in the Brotherhood of Equals and the following Benefit: The character gains
a +1 bonus on saves against spells and effects that have the air, earth, fire, or water descriptor.
If the character did that, "[s]uccessfully defended an item or structure important to the church" of Obad-Hai for +4 to his affiliation score, and hunted "down enemies of nature, or raze[d] the stronghold of a despoiler of nature" for a +8 to his affiliation score, he'd reach rank 2 in the Brotherhood and gain the following benefit: The character gains
a +4 bonus on checks made to resist bull rush, trip, or overrun attacks.
And so on. You've to pick which virtual affiliations matter for your campaign beforehand, tailor adventures to advance the virtual affiliations, and track campaign events that advance and penalize the character's virtual affiliation scores, but this should be fairly easy with the campaign revolving around but a single player's character.
- Others' opinions on the proper use of legendary sites and magical locations will vary, however. Theoretical optimization often assumes perfect conditions with goldfish DMs who approve anything printed. For example, writing Otyugh Hole (3,000 gp) on one's character sheet is sufficient for such theoretical characters to acquire the feat Iron Will.
- I imagine a New Game Plus version of your campaign that would cause the player to consider carefully which potions he wanted his character to combine after having learned accidentally of the rule with his first character. That's... kind of neat.