You might design a boss fight where the main enemy, once reduced to 0 Hit Points, transforms into a more powerful version that is a completely new creature, with its Hit Points and Mind Points fully restored.
The creature will only be considered "defeated" (and thus choose between escaping and surrendering) once all phases have been reduced to 0 Hit Points.
When you design a battle with multiple phases, the first one should be more of a warm-up (generally a normal or even easy challenge) and the “true” fight should only begin once the villain has transformed. If you want to go for the ultimate challenge, you could build a three-phase battle that goes from easy to normal and then culminates with a hard fight!
If you do this, it can be a good idea to give the heroes a free round of actions to prepare themselves between one phase and the other.
Just be mindful that a multi-phase battle can take a long time — plan accordingly and make sure you have time for it during the session!
You can give the boss battle a routine: the creatures perform actions in the same order, round after round. This option makes the battle slightly easier to manage as the Game Master, while also making it feel very video game-y.
It's not for everyone, but it can be an interesting solution to experiment with.
One final piece of advice: since crafting an interesting and challenging boss fight can take up to half an hour of work, prepare stats for your Villains and potential bosses in advance.
Updating an enemy to match the level of your group is much quicker than having to come up with the whole battle on the spot.