This would be a Multi-Cross. Just a note: this fanfic will focus more on Ike and Samus than on Link and Zelda. And Shiek is a boy. Disclaimer: I don't own SSBB or any other game references.

Crimea: "Ike, Soren, Rolf, what's taking you? We need to leave soon." Mist yelled
"Coming!" They replied.
"Remind me again why I must go to high school, Me and Soren are too old for that." Ike said, very irritated
"You've gotten an invitation. So you are going."
"I refuse to go. Go tell the staff that I am a busy mercenary commander taking care of bandits."
"Too bad. You are going even if I have to drag you to high school. I will take care of things here." Titania said. Ike quickly understood that there was no way out of this. So he agreed.

Altea: "Time for me to go to high school." Marth said to himself.

Elibe: "I guess it's time for me to go to high school." Roy said to himself.

Samus' Residence: Time for me to go.

Mushroom kingdom: "Rosalina, Daisy, it's time to go. We need to get there so we can get the cute boys before they are taken!"
"But Peach, we are going to learn, not flirt with guys."
"We have four hours of school, we start early so we finish by 10:00. Then we have the rest of the day to flirt, and we also have week-ends and holidays."
"Let's go, we need to get there early." They left.

Hyrule Castle: "Shiek, Minda, I can't wait. Let's get going!"
"Okay, thanks for letting us stay here for the night."
"No problem."

Some remote part of Hyrule: "Yay high school." DL said sarcastically. DZ was excited. She doesn't know DL yet.

Ordon Ranch: Link was ready to go. So was Ilia.

Smash Mansion: "Wow, this place is huge!"said Mist.
"It's terrible. Instead of this, they should have tents for the students and teach them how to fight." Ike said. He didn't want to be here.
"Let's go mingle with people!" Mist said.
"How about no." Ike and Soren said. Mist left and saw this cute guy that looked her age.
"H-hi, I'm Mist." Mist said, very flirtatiously.
"I'm Alan."

"Time to go and find some people to interact with." Marth said. He spotted a figure with blue hair and eyes, and a figure with black hair and a robe. When I walked closer, I noticed that the spiky blue haired person had a two handed sword in a sheath. "Hi, I'm Marth." He introduced himself.
"I'm Ike, this is Soren."

"Okay, girls, time find some girls, and some guys." Peach said. Samus came up behind them.
"I'm Samus."
"I'm Peach, this is Rosalina, and this is Daisy." Peach introduced her group. Then Zelda and Midna came in and introduced themselves. Shiek went over by the guys. The group walked around for a bit and saw a girl. She looked about a couple of years younger than them. They introduced themselves. "I'm Mist Greil. Have you seen a guy with spiky blue hair, blue eyes, a cape, and a two-handed sword? He's my brother."
"No, but I would like to meet some boys." They walked around trying to find Mist's brother. Then they found him in a group of guys. "There's my brother,Ike, and that black haired man with a robe is Soren." Ike and Soren turned around.
"Mist, why must you introduce me? I am about to break free and head back to the stronghold. I don't care what you say, but me and Soren are too old for this. Furthermore, we have bandits to take care of." Ike said, very irritated at his sister. "You are not about to leave and you know it."
"Ah, not a very bright one are you?'' Peach said. Ike just glared at her, then at Mist. Then he just walked off.
"He's 19. And I am just about as old as him. As you can tell, Ike cares more about battling with bandits and pirates. We finished off a war a year ago." Then Marth introduced himself, blushing because of Peach. She's beautiful. Peach also blushed. He's cute. Then Roy came along and introduced himself, followed by Link. DL and DZ met each other and fell in love. Ike finally returned to the group. "Come on Soren, we are leaving. We need to get back to Crimea."
"Ike, it's pointless, they've got the place secure. There's no escaping."
"Dang it." Then everyone introduced themselves to Ike. Well, those who haven't.

"Welcome Students, we are so excited to have you here. I am Principal Hand. If any of you wish to leave, too bad." When he said that, Ike had enough. He ran unsheathed Ragnell and ran over to Principal Hand and started attacking. After loosing a lot of health, Ike used Aether and restored his HP. "Tough one, aren't you."
"My sword skill was given to me by my father." After a while, Ike finally managed to weaken Principal Hand long enough to escape. He almost succeeded, if it wasn't for Soren, He used wind and brought Ike back to the group. Hand was finally healed by Mist. "Please excuse him sir, he has taken on too many responsibilities at too young a age. He is also stressed out because of his duty as a mercenary commander." Soren said. Hand seemed to understand. "Back to what I was saying, you will each get a schedule of your classes. This year You will different classes everyday we have school. On your schedule, you will see a room number. You must go ask for the keys. We will always have a spare in case you leave your keys somewhere including your dorm. Look for your names here." He pointed to tables that were filled with papers. Once everyone got their papers, They looked at their dorm number. Ike, Marth, Soren, Link, Roy, and Shiek were in the same room. The girls were in the room next door. "Soren, why did you stop me? I was so close."
"Ike, you know that Titania would tie you to her horse and drag you here if she had to. Escaping is useless."
"I'm going to die here." Ike said blankly. Then they departed and unpacked. Then the group, with the exception of Ike, met again.