Even two investigators isn't much of a challenge if you understand some of the fundamental game principles:
If you find this makes the base game easy, and you don't have other board expansions yet, I made these for this purpose (although they're fun regardless). Either way, good luck :'D
Enhancing the Base Game AOs
For playing the Base Game only and for enhancing the difficulty of the Base Game Ancient Ones:
I wouldn't play with the modified Doom Tracks if you have other board expansions (particularly Dunwich and Innsmouth), or use the following Elder Sign/Encounter rule:
Doom tokens can not be removed from the doom track by any means prior to final combat (that means no South Church exploit, and no Elder Sign hunting). This makes it so you can't just play out the clock for a guaranteed win. Elder Signs are used as normal, but they don't reduce the doom track.
Optional: ban the use of clues with the fight skill and/or the shotgun during final combat.
Starting Doom Tokens for base game Ancient Ones [with the base board only]:
Azathoth: 5 [if you are not just playing the base game, 3]
Yog Sothoth: 2
Shub Niggurath: 3
Yig: Investigators can not be blessed during games against him (Sister Mary is an exception to this rule). Twice as many successes as normal are required to remove a doom token from his doom track.
Cultists are fast.
Ithaqua: gains physical and magical resistance.
Each round of combat with a cultist, roll a die for each weapon or spell you are using, on a failure, it is lost.
Azathoth: Start him with 5 or 3 doom tokens.
Cultists and Maniacs deal four damage to an investigator who defeats them and are stalkers.
Cthulhu: when he reaches 7 doom tokens, his ability reduces all investigators maximum stamina and sanity by 2 instead.
Star Spawn have their toughness increased by two. If they are adjacent to an Elder Sign, they will move onto it if their movement is shown during the mythos phase, ignoring investigators and arrows. If they are still on the Elder Sign during the next mythos phase, remove it from the board. If they defeat an investigator in combat and are permanently on the board, they immediately move one space closer to the nearest Elder Sign (player's choice if there is a tie), following an arrow, or directly (if they are directly adjacent). They can not be taken as monster trophies. If they are defeated, return them to the cup. If they are placed in the outskirts, substitute them with any non-Star Spawn monster on the board that is not in the Sky— if there is a Cultist on the board, a Cultist must be chosen.
Nyarlathotep: is magically and physically immune and requires twice as many successes as normal to remove doom tokens from his doom track.
If you defeat a Cultist, immediately search the monster cup for a random Mask, and fight or evade it as well. If the Cultist was on the board, the Mask remains on the board if undefeated, if not, return it to the cup.
Hastur: raise the terror track to four at the start of the game.
If a Cultist is in the sky, moves, and is unable to leave the sky (due to lack of investigators in the street), raise the terror level by one. When a Cultist is defeated, all investigators lose one clue.
Yog Sothoth: gains physical resistance. Flip all gates against him upside down until investigators enter them, increase their modifiers by -1.
Before investigators in an Other World draw their first encounter they must fight or evade a random monster from the monster cup. If this causes them to be devoured, add a doom token to the doom track.
Shub Niggurath: gains magical resistance. His final combat attack require investigators to lose 3 monster trophies.
Dark Young have their toughness increased an additional one, are Endless, and are not counted against the monster limit. Dhole moves like a Hound of Tindalos, is not counted against the monster limit, and is Endless. Every time a Cultist is defeated, roll a die, on a 1-3 search the cup and place the Dhole on the open gate with the least number of monsters on it (players choice if a tie). The Dhole and Dark Youngs can not be taken as trophies.