I've got a good portion of Ch 2 written, but it needs work. Speaking of work, I gotta go to it, so here is what I have so far, the next part before publishing is the actual entry of the ships into Equestria. Let me know how it feels, because it doesn't feel right to me just yet.

"Houston Command, this is the Santa Maria, unknown anomaly is pulling us toward the planet's surface at an exponentially increasing rate of speed, time to impact, now only eight hours and point of no return at the seven hour mark. how copy?"

Whistling and static permeated Mikko's headset, as he tried reaching Earth for what felt like the millionth time. Finally this time, a voice tried cutting through the interference, "Santa—and, only partial copy. Coronal Ma—ion heading for Earth and Mar— irty and seven hundred kilometers per second. Recommend ejection of landing—in twenty seven minutes, do you copy?

It took Mikko a couple minutes to decipher what had been said to him, but in a moment's time it all became clear: the sun threw off part of its surface and it was heading straight for Mars... with Earth right in its path. But what was recommended to him was asinine. To eject the landing pod at the rate of speed they were travelling would tear the pod and the third stage booster behind them apart. On top of that, Mikko had spent nearly three quarters of the thruster fuel trying to get them back on course. Even with Mars' thin atmosphere, they would skip across it and into deep space like a flat rock on a pond's surface.

"C-command, negative on ejection, speed and trajectory unsuitable for positive landing."

The radio crackled and whistled some more until the voice of the Flight Chief came on, with just enough time for no interference to make the message unclear, "Captain... right now it's your only hope. With what we read from your on board computer, even if you are able to change your course right now, it won't be enough. This flare is huge, and coming for both us here and you. We're taking shelter here, but we're reading such a massive spike in radiation and force, it'll be a miracle if the magnetic field holds."

A loud whine interrupted him and Mikko nearly threw his headset across the ship it was so loud. He readjusted it and turned the volume down a bit as the last of the message came through, —not going to sugar coat this Cap—you will land only moments before it reaches you. If you make—shelter immediately. Good luck, Toivo, and Godspeed."

Those final words cut through Mikko, pang in his stomach and head throbbed as the severity of the situation took hold. He unbuckled his harness and leaped from the cockpit to the hibernation bay. He grabbed a handle bar next to Kathy's sleeping form, bringing himself to face her. Running a hand down the glass in front of her, his head thunked against the door of the pod.

He whispered to her, "I... I don't know if I'll talk to you again. I know you can't hear me, but I just had to say I love you one more time." With that, he kissed the glass, and pushed back towards the cockpit to start the separation sequence.

Twenty four soldiers stood at attention inside Celestia's castle, their matte-black armor reflecting no light from the solitary candle in the dark dungeon room. Before them sat three princesses, Celestia, Luna, and now Twilight Sparkle. Both Luna and Twilight had their eyes closed, focusing on the magical force emanating from the forest in the valley below. Celestia how ever, stared unblinking at the elite force. She cleared her throat and took a step towards the Sergeant at the front of the platoon.

"Sergeant Night Silence, I have asked you and your soldiers here because we require your assistance. You're the best of the best, and something may be coming that will be difficult even for yourselves. As you know, nothing I am about to say will ever leave this room. What I will say has not even been told to Twilight yet. What I will say... will change how you look upon Equestria forever. If any of you wish to excuse yourselves, you may do so, but do so now."

The Sergeant looked at his soldiers, none of whom moved a single muscle. He turned back to the princess and smiled. "No pony is leaving, Your Highness. We took and oath to do what no other pony guard would or could do, and we'll hold that oath to the death."

The surge of pride Celestia felt brought a kind, albeit brief smile to her face. As the smile faded, she nodded. "Very well, I will begin. You all know of the mission I had told you of months prior, where if Princess Twilight failed to return before the Mirror sealed, you would be sent in on the next opening to retrieve her, correct?"

A chorus of "Yes, Ma'ams" rang through the tiny room before she continued, "Well, I must inform you that there is another mirror. One more ancient than the one Twilight ventured through, and older than either myself or Luna. It is much bigger, and as far as we know, something or someone, is coming through it."

For once, the rigid soldiers broke their stances as they looked at one another. Even the Sergeant managed to blink a couple times as the odd news registered. Celestia allowed it soak in, before furthering her explanation. "This mirror... is where Luna and myself came from. When we left the place where the mirror leads, it was a desolate and unlivable world. What could survive such conditions scares me, and what frightens me more, is that it could be coming here. Whatever it is, it knows magic, otherwise it could not open the mirror. As of right now, that is what I can share with you, but know that you must be ready to face anything that could come through—"

The Sergeant spoke up as a thought cross his mind, "Princess, excuse the interruption, but could we not go through it ourselves and stop whatever it is from coming through?"

The princess smiled and shook her head. "Unfortunately, this is not as similar to the smaller mirror. It is one way only, so if this thing comes through, it's here to stay."

The Sergeant shrank back and stood next to the pony soldier on the end. "Very well, Your Highness, we will do whatever you ask of us."

"Good. It shall reach maximum power in just under four hours. Be ready to airship to the mirror just before it does."

Mikko was back in the cockpit, but couldn't do anything more than watch what unfolded, the booster behind having been ejected, somehow with minimal damage. Unfortunately, the ejection process triggered the Pinta's and the Santa Clara's ejection as well, so now both of their pods would crash near the Santa Maria's crash zone, further hightening the danger.

The camera on top of the pod had long since gone off line, yet the abrupt cut off of all communications, even the locator beacon, from Earth. The Ejection had already reached Earth and wasn't far behind himself. He had tried playing his music over the speakers, but all power was transferred to life support for the pods, Mikko himself sitting in his suit. The ship had reached such a speed that he wondered why they had yet to break apart, and was only minutes away from entering the atmosphere.

A shadow overcame the ship, and Mikko stared wide eyed as another strangeness appeared before him. Phobos, the larger moon of Mars, was whipping around Mars at an alarming rate of speed. Not only was it going too fast and too close for Mikko's liking, he noticed it was completely out of its regular orbit. Watching it for a moment, he ran a few quick calculations in his head with his yes shut. They snapped back open when he realized with where it was heading, it would strike them before Mars even had a chance to tear their lives away. Knowing he had no options, he swallowed hard, and began reciting the Lord's Prayer out loud.

"Our father, who art in Heaven, hallowed be thy name. Thy Kingdom come, Thy will be done, one Earth as it is in Heaven."

The shadow passed ever closer, though Mikko payed it no mind, his eyes focused only on the planet's surface. He shook his head and yelled the next lines of prayer, "Give us this day our daily bread! And forgive us our trespasses! As we forgive those who trespass against us!"

His eyes clenched shut. He could nearly feel the looming presence of the moon coming closer. "Lead us not into temptation, but deliver us from evil!"

The seconds until death ticked away in Mikko's head. "For thine is the Kingdom!"

Less than ten seconds. "And the power!"

Five seconds. "And the glory, forever and ever!"

Boom...

Yet, no "boom" came. Mikko, his breathing heavy and sweat dripping from his forehead, peeked one eye ever so slightly open. "A... men?"

The moon was directly in front of the ship and had stopped moving. It was stopped dead in its tracks.

"This... is impossible!" Mikko yelled in frustration. "How is this possible?

He banged his helmeted head on the console a few times, the last one forcing the glass of his visor to split his forehead open and halting his self harm. He lay there for a moment, countless possibilities running through his mind, yet none of them coming close to explaining what was happening. But one more thought crossed his mind. He forgot the pain in his head, and flung it back up to look at any point of reference outside.

The ships had stopped moving. He pulled the radar up again, and saw that indeed, they were staying at two kilometers above Phobos' surface. He strained his head at the side window and saw the Pinta less than two hundred meters away, seemingly frozen in time. Mikko plopped back down into his chair. He leaned his bleeding head against a gloved hand and laughed.

"All I wanted to do is fly again. Now I'm here, I just want to go to the ground and never be airborne again."

He leaned back and closed his eyes, number running through his head, wondering how the abrupt stop from thousands of kilometers an hour didn't liquefy his body. Or even move him for that matter. He slid his gold tinted visor down as the sunlight outside began to lighten against his eyelids. In a couple moments, he thought of how they weren't even facing the sun.

His eyes flew open once again, although immediately slammed shut at the blinding light in front of him. His eyes squinted he tried seeing outside the windows, and was again floored by what he saw. The light blinding him was not from the sun, but from a beam of blue light stretching from outside of his view from the cockpit, and lighting up the entirety of Phobos. He leaned forward to see where the light came from, but mingling outside the ship with the blue light was the white-yellow plasma soaring through space at incredible speeds. The plasma joined with the blue light, turning it green.

Mikko pressed his face against the visor and the window and stared, ignoring the light spots forming in his eyes. Suddenly he was thrown back into the seat with so much force, he thought his back was broken. The light outside brightened, as the ship itself moved towards the moon at the speeds it traveled before. Mikko uttered one final phrase before the light enveloped him: "Help me, God."

I know there's spelling mistakes. I'll fix em before I publish.

Sorry to be "that guy," but in the first chapter...

'"Two. One." The rumbling turned to violent shaking as the locking arms released the Santa Maria from it's Earthly bounds.'

You used the wrong "its". "Its" shows possession, "it's" is a contraction of "it is" or "it was."

Also...

"Mikko's heart stopped as he gazed into the abyss, the abyss itself gazing into he. "

I'm sorry, but I think that last part sounds corny as all get-out. The sentence would be better without it.