Under the City: Twins in Pursuit
Without a doubt, this is the worst mission in the game. There's no real strategy to it: You basically need to clear a path for Niobe and block the path of the oncoming ghostafarian twins. You do this by blowing up the cars of innocent civilians, both in front of and in back of your automobile.
Unfortunately, Niobe won't avoid blocked roads, so you'll just have to hope that any cars you manage to dispose of actually land in a lane other than your own. Just keep firing at anything that looks like it might be a problem, and hope you make it to the end. If Niobe gets blocked, the mission will almost certainly fail. You have no control over her driving, though, so you'll just have to hope you can keep the coast clear and that the cars you dispose of land in a different lane.
Zen Garden: Trinity and Ghost
This fight is relatively easy, but it takes awhile--just remember to block and counterattack when given the opportunity. If you get hurt, run to a new location and wait for Trinity to approach. Note that you can lose, but it also doesn't matter. Ghost just needs to work out some of that unrequited love.
The Freeway: Chase Morpheus
This mission is incredibly easy, but it makes for a pretty fun break from all the recent karate. And it redeems the awful "Twins in Pursuit" mission. As Ghost, you just need to shoot everything and anything you see. No joke. You have the police and agents on your tail, so you need to block their path with every car you pass. Just keep shooting vehicles as they pass by, and occasionally swing forward to clear out the police cruisers ahead. Perhaps the residents of Zion have a new plan to win the war against the machines: Just kill everyone in their power supply.
Once the agents back off, focus your attention ahead, because you need to clear a path for Niobe to make it to the truck.
The Freeway: The Truck
Again, this is an easy and fun mission. Your plan is the same as in the preceding mission: Just shoot at and destroy everything. But mostly you want to eliminate every police car in sight. Once Niobe reaches the truck, the mission ends.