Majik1387 said:
So then what was Scott's excuse for abscence? (I refuse to say death)
There are plenty of scenarios that would make sense that wouldn't contradict most of the movie's footage until the battle of Alcatraz, depending on how you want to write it up.
The general consensus on this forum and others seems to be that Jean wasn't quite as good at holding back his optic beams as she thought she would be, or that by holding them back it was causing side effects, like terrible pain to his temples. Which would explain why in the final moments of that scene you see him struggling or in pain. Jean lost her concentration, became agitated, Scott telling her that it hurts and to stop what she's doing. As she becomes agitated random things start levitating in the air, water starts to vaporize from the lake (we know this kind of stuff happens whenever she has nightmares, like shaking the bedroom or books and furniture flying around).
Before you know it, his optic beams suddenly come back and he fires at her at point blank range. She reacts by reflex the way you would if someone were to toss something at your head. Puts up her arm and deflects it, just like she did when Scott attacked her inside the dam. Except this time she's alot more powerful, so the reaction is much for violent and painful for poor Scott. He gets capatulted back like he did inside the dam but much further this time, into that wooded area. Branches and bushes break his fall. Definitely out of sight. Jean's knocked back, falls off that rocky outcropping and hits her head, or just passes out from shock.
There are variations of this. They could have both been found lying close together but Scott's injuries needed treatment at a real hospital so he'd be out of commission for a while. Or Scott was thrown so far into the woods that they couldn't find him. The book states there was a tracking device in the motorcycle but not on Scott. And Wolverine's sense of smell doesn't work if the wind blows the wrong way, and you can't follow a trail if there isn't one to begin with.
Or by the time they got there, Scott could have already left the area, groping around blindly trying to find his way. He certainly would have some training to know what to do if he ever loses his visor or glasses.
Remember the dialogue at the medical bay later on? Only a small change is needed. Logan would simply ask Jean "what happened to Scott?", not knowing that she didn't know. She's dazed and shocked again and only sees flashbacks: they're together hugging, and suddenly there's a bright flash and all goes black. She could have been convinced she killed him and never had a chance to clear things up. Angry and upset, she blows Logan against the wall and walks out and to her house just as before.
Scott could be missing in action for as long as you want him to be. He could be in the hospital for a while, , lost in the wilderness. Either way would be effective to remove him from the story for now or have people think he's dead. They could either decide to look for him again and this time manage to find him, or he's rescued when he manages to run into other people: Hikers, motorists, park rangers, etc.
Had Cerebro been available, they could have used that to check for sure. They could have said "Scott's dead", and that would have been that. But they didn't, so it gives us another hole to exploit

There are indeed lots of possibilities which are reasonable and believable and wouldn't contradict the film until the end, where you now have the opportunity to make the outcome of the story much more interesting.
90% of this movie was based on a script that the writers admitted was just a rough draft put together in about 80 minutes, and it shows. I doubt they ever sat down to think about the details of these scenes or what they meant. I get the feeling they got more input from the actual cast members than what they could have thought up themselves.
I'd pay money to see the look on Jean's face or to read what goes on in her head when she sees Scott emerge from the blackbird at Worthington labs, realizing that he's alive after all.