So here's my idea. What if the Blacklight virus took over Mercer's mind and that's why he turned Heller into host #2? His whole demeanor changed between Prototype 1 and 2, so maybe the Blacklight put him in a kind of psychological stasis to ensure it's goals were met. Mercer could have awakened when Blacklight tried to kill Heller and changed the strain injected into him to make him a stronger host than Mercer's body, thus leading Heller to go after "Mercer" (Blacklight).
Now, what if while Heller was tracking down Mercer, the Blacklight Mercer infected Amaya? We see her get sick in the final cutscene of P2, so Heller injecting her could be slowly stabilizing her health by fighting the Blacklight strain from Mercer. As Amaya grows and starts discovering her powers, she might start gaining control over both strains of vice-versa. This would lead to an inner struggle as all three parties fight for control, making her behave erratically, sometimes killing for pleasure, but also ocasionally saving people from the virus. Halfway through the game, the dual strain of the virus inside her body could be explained via cutscene or something and you could choose one of three paths: Virus, Cure, or Host.
The Virus path would be full on Blacklight infection. Infect as many humans as possible, kill the Blackwatch, consume anything that can strengthen you. Destroy the cure supply (haven't thought of a name for it yet) and finally take down the whole organization that created and tried to destroy the virus.
The Cure path would be it's opposite: take down every Hive, Infected, Evolved, and Blackwatch researcher trying to continue the infection. Take control of Blackwatch Commanders to give complex attack orders, summon airstrikes and APCs, and eventually absorb a small portion of cure to become the Anti-virus and take down every last bit of the infection once and for all by injecting your own new strain into Infected.
Host path would mean you continue on your own way. You take the most convenient path to achieve your own goals, sometimes supressing either or both Heller and Mercer strains to research if you may be cured, but sometimes failing and falling victim to either of their control and doing things you might regret.
Phoenix- Large bird-like Infected that swoop down and attack unsuspecting prey. Usually in flocks ranging from 5-15. Two variants: Bomber (throws exploding fireballs and objects it picks up) and Streamers (shoot jets of flame and have a fiery aura). First boss encounter is a giant version of this that has both powers and gives Gliding ability.
Lurker- Smaller, long-range Brawlers that use tendrils to attack from far away. Leader Hunters and Shriekers can summon them along with their pack.
Kamikaze- Infected Super Soldiers that run towards you and explode after a certain amount of damage is dealt.
Master Hydra- Giant octopus-like creature that summons more tentacles the more you hit it. It's only weak spot is it's eye and you can only kill it by grappling it's own tentacles into it.
Infection Pod- Shoots out Infected and clouds of virus until it is destroyed.
Blackwatch Enlightened- Regular soldiers on par with Super Soldiers because of the Blacklight virus, but not quite Evolved. Start out by using weapons but then rely on Musclemass.
Musclemass- First power you get when you discover you are a Blacklight host. Used to destroy wooden and glass obstacles and low-mid damage to enemies. Strong attack is a shockwave-creating kick to the ground (if in the air) or enemy (on ground)
Claws- Second power obtained. Recieved by consuming a Leader Hunter. Strong attack is Pounce. Upgrades increase number from one to five claws, increasing damage.
Blade- Third power obtained. Recieved by consuming Evolved Commander. Strong attack is Flurry, a sphere of slashes that knocks opponents back. Upgrades increase size and damage, also swinging speed.
Shield- Fourth Power obtained. Recieved from consuming Juggernaut. Upgrades increase spikiness and add a dash attack.
Hammerfist- Fifth Power obtained. Recieved by absorbing infected Super Soldier. Strong attack is a large shockwave that summons spikes to knock opponents into the air. Upgrades increase size and damage.
Armor- Sixth power obtained. Recieved after getting shot by Thermobaric Tank. Upgrades increase health and can help you take up to 3 regular mussiles before fading away. Takes away Gliding and Flight.
Tendrils- Seventh power obtained. Recieved by absorbing 10 Lurkers in the quest "Lurking in the Shadows"
Bio-bomb- Obtained with Tendrils. Throw at target to draw in objects to attack it. Upgrades increase range and damage from drawn in objects.
Wings- Eighth power obtained. Recieved after consuming Blackwatch operative Condor with his experimental flight suit. Strong attack throws sharp feathers. Upgrades increase time you can fly (final upgrade is three minutes) and finally add a small explosion to feathers.
Whipfist- Obtained with Wings. Upgrades increase range and damage.
Posession- Tenth power obtained. Recieved by consuming Goliath. Forces nearby lesser Infected to fight alongside you. Upgrades increase range and time Infected stay under your control.
Cheats (in-game Extras menu) (unlocked by finding Secrets):
Look! Up in the sky!- Infinite flight (20 Secrets)
Regenerate Biomass- Your Biomass bar refills slowly (15 Secrets)
Like a Tank- Armor and Shield don't break (17 Secrets)
Apocalypse- Everything is Infected (12 Secrets)
"Safe"- Much more Soldiers and Blackwatch (12 Secrets)
Wanted- Always pursued (7 Secrets)
Ultimate Life Form- Infinite Health (50 Secrets)
Boom Boom- Everything explodes (no extra damage, only slight stagger) (17 Secrets)
Original Host- Alex Mercer skin (10 Secrets)
Stronger Than You- James Heller skin (10 Secrets)
Darkest Days- Only red cloudy sky (5 Secrets)
Beautiful Day for a Picnic- Clear, blue skies (5 Secrets)
Embracing Your Darkness- Blacklight Amaya skin (basically the same change between regular Mercer and Prototype 2 Mercer: glowing eyes, infection cloud, infected arms/legs) (15 Secrets)
Black Boxes (50)
Hives (15) (regenerate after a time, logo on map adds star to previously destroyed Hive)
Blackwatch Bases (21) (3 types: APC, Helicopter, Personnel, must destroy at least 50% of base to draw out commander)
Landmarks (50) (I know they're annoying, but it's not 200 like before)