At no point in the story do the Marines fight Cell. In fact both work under the same juristiction (the Department of Defence) and when that is rescinded due to Jacob Hargreaves' actions, they all disarm and relinquish command without any trouble. In fact Hargreaves even orders the remaining Cell forces to fight alongside Alcatraz before he dies, and they do so.

Both of them have the same aims (to fight the Ceph) and they're only after you in the single player because they're a rogue faction commanded by Lockheart with a personal grudge due to thinking you're Prophet who murdered scores of them. They at no point go after the Marines. In the multiplayer they're actually commanded by Strickland, who it turns out is an undercover CIA agent on the Marine's side, making this even more nonsensical.

Story lines are so boring I fell asleep during your post. IMO the whole story could be Bob went from point A to point B.

Multiplayer doesn't need to make sense story wise, it isn't canon, and please, if you insert a spoiler, tell people with a SPOILER ALERT.

What exactly is the point of this pointless thread?

He's trying to come up with a Red Vs. Blue scenario apparently..