Metroid Prime 4: Beyond walkthrough pt. 9 (Chrono Tower)
Defeat Sylux and finish the game
When you give the order(s), you’ll launch your assault on Chrono Tower. Once the forcefield is down, it’s time to head inside and finish off the game.
Chrono Tower
You’ll get four Guardian guides this time. Follow them into the tower.

When you hit the Lamorn statue, scan it for one more cutscene.
In the next room, scan everything and activate the sphere in the middle of the room. Take the elevator up. Check in with your friends on the ride.

At the top, look to the left of the statue for a Psychic Rail to scan and activate. Take it up to the Pinnacle.
In the room at the top, scan everything, and then loop around to the other side. Hit the terminal to fire up the teleporter.
Walk toward the arch.
Sylux final boss fight
And then Sylux shows up.

This boss fight is divided into three phases with a checkpoint between the first and second phase. Which is good, because the first phase sucks.
Phase 1
The first phase also has multiple sub-phases for extra fun.

When Sylux is glowing green, his nanobot swarm will form tentacles with weak points at the tips. Whenever this happens, your job is to shoot the end of the tentacle until you destroy the tip and then lasso it to pull it off. This also gets you some ammo and health when this happens, so make sure to charge up a shot to collect them.
When all of the tentacles are gone, Sylux will be exposed for a few seconds. Super Missile him as much as you can before he reactivates his tentacles.

For the next sub-phases, he’ll turn his tentacles into elemental dragon heads and start dealing elemental area damage. You can destroy heads during this, but it takes a lot of shooting and I’ve only done it a few times in my (so, so many) attempts at this fight.
Also, the heads don’t seem to be weak to their opposite elements — fire is not weak to ice, for example — so there’s no shortcut here.

Throughout these phases (especially the Thunder phases), your primary goal is to make sure the rest of your crew doesn’t die. The second you see someone’s health bar go red, switch to the scanner and go target them to get them back on their feet.
You can and will lose this fight if one of them dies, and they are terrible at not getting hit.

Eventually, Sylux will switch back to green tentacles and the process will start over. There are two things to watch out for here: when he bundles the tentacles into a sweeping attack and when he spins.
For the sweeps, you just have to jump over it — just make sure to jump earlier than you might expect because the timing is weird.
For the spinning attacks, you can Morph Ball Boost away or just carefully time a Dodge. The biggest problem you’ll run into is running into a teammate.
Phase 2
After you deal enough damage, Sylux will tackle you into a wormhole-tunnel-thing. This is a mercifully slower-paced fight which is nice, because the controls suck during it.

You can no longer lock on, so save your missiles. Your first job is just to avoid attacks. Sylux will summon discs from the walls that give you just enough time to avoid them. If you watch him carefully, he telegraphs these pretty well.

He’ll also occasionally summon a pair of rotating beams. When this happens, switch to scanner and fire a Control Beam between them to hit Sylux.
Most of the times you hit him, he’ll drop some health. Picking it up is a different story, though, and the charge beam vacuum only sometimes works. Just do your best.
Keep peppering him as you go until you deal enough damage to move to the final phase.
Phase 3

Both the good and the bad news (mostly good if I'm being honest) for the final phase is that you’re facing Sylux one-on-one. You’ve still got a long way to go to finish the fight, though, and he’s got some nasty tricks.
For this phase, things might start to get a little desperate (or, at the very least, I was getting desperate to finish it), so save your missiles. Use them to repeatedly activate your Legacy Shield — switch to scanner and hold R.

Use whatever Shot you want to keep beating him up while you dodge attacks — mostly jumping over waves, dodging rushes, and Morph Ball-ing under beams.

I used the Super Thunder Shot mostly because it’s harder to miss with it and because your attacks don't actually do anything to interrupt him, so he'll still be moving around a lot.

After a bit, he’ll vanish into a wormhole, and then reappear while charging up these black hole-like attacks. When you see him start, fire a Control Beam. You’ll have to steer it down the whole time to avoid it getting sucked into the black hole. Hit Sylux to cancel out the attack.

He also has a really annoying not-Morph-Ball mode that he’ll use. You mostly can’t shoot him when he’s like that. When he hits you, he’ll steal an Energy Tank. If (when) you can't dodge his charges, your job is to Morph Ball Boost into him and reclaim it. It’s a pain.
But wait, there’s more!
It might be tempting to put your controller down after that hard fight. You might want to, say, switch back to writing up the guide for the boss fight. Or maybe you just weren’t paying particularly close attention.
There’s a not-quick time event in the closing cinematic. And if you don’t hit the button in time, you’ll have to restart the fight from phase 2.
Yes, both Ryan and I found this out the hard way. Yes, it’s a weird design decision. (Apropos of nothing, Most Frustrating Game is a category in our recently announced Rogueie Awards.)

There’s no choice here. You have to push the teleport button. And you have to do it kind of quickly. Otherwise, you will lose the fight.
Push the button, finish the cutscene, and you’ll get credits.

After the credits and an after action report, you'll get one final cutscene.