Doom Komodo is at Level 1, same as Bob, but uses an HP to One attack. He comes back later at Level 1, while the heroes have reached the Cap of Level 100 and got the best Mons.
Doom Komodo is downgraded to a Boss Battle from being completely unbeatable.
Downplayed: Doom Komodo is a demi-god compared to Prince bob during their first fight. When they have a rematch, Prince Bob has taken many levels in badass and brought his team while Doom Komodo has not, and as a result Prince Bob beats Doom Komodo, but it's still an extremely difficult fight that almost kills Prince Bob.
Doom Komodo, just like the other enemies, can't increase in level, even though he's not one of the Mons.
Alternatively, Doom Komodo is the toughest being in his ecological niche; he has no reason to believe the hero will improve so drastically, and no good sparring partners to up his own game.
Inverted: The Sorting Algorithm of Evil is in play, but it's the heroes who remain static while their opponents steadily grow in power.
Subverted: Doom Komodo gets even stronger the third time around.
Double Subverted: After Bob defeats a lot of the enemy's resources, Doom Komodo stays static between the third and final fights.
Parodied: Doom Komodo is revealed to have been called back from his vacation for the second battle; he hasn't been training for the rematch.
Zig Zagged: Level 50 Lamia is easily defeated by the level 65 heroes. However, she then becomes a level 80 One-Winged Angel, but then she sends down high XP minions and Alice and Bob Level Up to Level 90 and defeat Lamia in one swoop. Then she becomes a Level 95 Extra Winged Angel and defeats the heroes. Then Alice and Bob go off to find her and go into Level 100 and defeat her.
Enforced: If the audience is not given some semi-plausible reason to believe that the heroes will beat the villain the second time around, they will simply give up hope and stop playing.
Lampshaded: "In the three years since we first met, I've been fighting monsters and training for combat while you have been watching TV. Do you really think you're going to win this time?"
Invoked: Emperor Evulz wants to test the potential of a given group to judge if they are worth assimilating. He builds a copy of Doom Komodo stronger than the current group and sets them lose - if they are able to advance enough to defeat them they passed.
Exploited: Doom Komodo has a Xanatos Gambit going on - he drains the power of heroes that level grind and slaughters them. He skips straight to slaughtering the ones that don't level grind.
Implied: The villain avoids facing Bob after his defeat, instead throwing up seemingly insane defenses when the hero arrives, starting after the second battle where he manages to win.
Deconstructed: Doom Komodo is easily defeated by the heroes because they've been getting stronger while he stays static.
Reconstructed: Doom Komodo was so far ahead of the heroes that he either didn't bother to improve or had less room for improvement. He's still better than any one of the heroes so they Zerg Rush him.
Plotted A Good Waste: The Empire has been in power for so long that their forces have grown complacent and overconfident; this is translated into gameplay by having most major villains never gain levels, while more Genre Savvy villians do scale to prove a greater threat to the party — and to players lulled into their own false sense of security by their own victories.