"Shadow, my son. If you're listening to this, then the worst has happened… You need to know the truth. The government plans to shut down this research facility. The government plans to cease all of our research… and imprison all who know about you. I made a terrible mistake, Shadow. It's all my fault… making contact with that comet."

As they watched in silence, Commander Tower was perplexed by what he was seeing and hearing. "Professor Gerald?" What was this message? Looking at the background, it was clearly recorded aboard the Space Colony ARK, and unlike his final message to all of humanity, the Professor seemed healthy, and far less menacing.

"The government… shut down the ARK?" Hope asked. "I thought the ARK was shut down because of an accident."

"That was the official report," the President confirmed, "But to be honest, even I don't know that much about it. Details about that incident are hidden, and what little is there is vague."

Tower didn't want to admit it, but he was right. The incident on the ARK was kept top-secret. Even when he was a General, there was little he could find regarding that day. Of course, since he had seen it all first-hand, it was never really necessary for him to read the report itself. But what Professor Gerald was saying… "They must have known about Project: Shadow before the disaster happened, and were simply too late to stop it."

"Now, listen very carefully…" Professor Gerald continued. "In fifty years, the Black Comet will return… They plan to harness its powers to destroy this planet! The only way to stop them, was to develop a way to use the very power they intended to use against them."

"That's it! It's brilliant!" Eggman's voice sounded over the radio.

"The very power they intended to use…" Hope mused. The Black Arms were hunting Chaos Emeralds, so that means… "The Eclipse Cannon!"

The message continued. "Shadow, it's up to you, and only you can stop them! I developed the Eclipse Cannon… It's the only weapon that can destroy that Black Comet. Shadow, you are the only hope… to save mankind as we know it. The future of this planet, depends on… you!"

Tower held a hand to his forehead, trying to make sense of all of this. Shadow was created to save the planet? But if that was the case, how did that explain what had happened on the ARK? The Eclipse Cannon – a weapon powerful enough to destroy planets – was built for good? This all had to be a trick! Professor Gerald was the mad scientist who had tried to destroy the planet, there was no good reason to take him at his word!

"Don't worry, Grandfather!"

Tower gasped. "Maria!"

Maria appeared beside Gerald in the video as the static began to worsen. "Shadow and I will protect this planet. Right, Shadow?"

Static overtook the rest of the message, and the signal was soon lost. Tower felt like he was having a very bad dream. Nothing made any sense to him. Maria herself believed that Shadow was going to be this planet's protector, and with what the Professor had said about the government planning to shut down Project: Shadow, even before the incident had taken place…

"My great-grandfather…" Tears welled in Hope's eyes as she stared at the now-blank screens. She wiped them away quickly, and turned to the Commander. "He was… trying to save us."

"That can't be…" was Tower's response, his voice so low that Hope couldn't even hear it. "If that was the case, then what was the that tragedy fifty years ago?"

"I think things are about to get worse, before they get better," the President said with a great sigh. "One thing's for certain, though… it might already be too late. The Black Comet has already reached our planet, and now-"

"Don't give up just yet, Mr. President!" Sonic's voice sounded over the radio.

"We can move again!" Amy chimed in.

"The effects of the gas must have only been temporary," Tails concluded. "We're evacuating the comet. There's not much we can do right now, but we still have Shadow!"

"Shadow… Will he really be enough, all on his own?" the President asked.

"Do you even hear yourself?!" Eggman shouted. "Shadow was the finest creation of my grandfather, the most brilliant mind of his time! If he made Shadow to save us, then there's nothing to worry about!"

Hope nodded. "He's right, for once! Shadow is… someone who won't give up, no matter what! I believe in him!"

"Commander, Mr. President!" an agent shouted. "We're receiving a feed from Central City! Something has appeared in the skies, above the Black Comet!"

An image was shown on the monitor, of a titanic-sized, two-headed creature floating in the skies, two large wings the sizes of planes keeping it afloat. As it roared, buildings, cars and other bits of debris were lifted and surrounded it.

Just then, a golden glow shot out of the Black Comet. After enhancing the image, everyone could see that it was Shadow, powered into his Super state using the seven Chaos Emeralds.

"There he is!" Hope cheered.

"Good luck, Shadow," the President said, clenching his fist.

The others in the room joined Hope in cheering Shadow on, shouting words of encouragement despite knowing he couldn't hear them. Tower simply watched in silence, his mind a maelstrom of thoughts as he tried to make sense of the events fifty years. As he tried to come to any conclusion, other than the one he desperately wanted to avoid.

Shadow fired a volley of Chaos Spears at the debris and made his way to the creature, who had identified itself as Devil Doom. He fired a charged spear into the eye on one of its head, and the eye quickly retreated to the other head. Shadow gave chase, but was cut off by a barrage of laser blasts that knocked him away.

Devil Doom initiated Chaos Control, and moved himself elsewhere over the city. Shadow grunted and gave chase, using his Chaos Spear to blow away more debris that was thrown into his path. Devil Doom raised its head, and then shot a jet of flames at Shadow, enveloping him in fire. This did not phase Shadow, though, who simply charged another Chaos Spear and launched it at the eye, which retreated again to the other head.

"I see… I seem to have underestimated the true power of the Emeralds," Devil Doom's voice roared over the feed.

Tower narrowed his eyes as he noticed something. Black Alien gunships began to approach the site where Shadow and Devil Doom were fighting, and he rushed forward to give new orders. "Signal all troops in and around Central City!" he shouted, surprising everybody. "If they can move, tell them to shoot down those gunships! Furthermore, I'm rescinding my previous order to shoot Shadow on-site!"

"Yes, sir!" Agents scrambled to relay orders to all squads that they could still reach in the Central City area. Soon, fighter jets deviated from their previous flightpaths to intercept the approaching gunships, and soldiers in Central City that could move again started to direct their turrets upwards.

"Even if it's only a little, we need to buy him every second that we can!" Tower gritted his teeth. "If his Super form runs out before he finishes this battle, then all hope will truly be lost…"

Shadow noticed the gunships approaching, and was preparing to avoid them, but before they had a chance to fire on the hedgehog, GUN's own ships began shooting them down, and support from the surface slowed many of the rest of them.

Devil Doom noticed this as well, and began firing large pieces of debris at the GUN crafts, as well as raining fire down on the streets below. Enraged, Shadow used the opening to reach Devil Doom's eye and fired another Chaos Spear. It retreated again, but Shadow chased it down, deftly avoiding the lasers now that he knew they were coming, and fired again.

Devil Doom attempted to use Chaos Control again, but Shadow reached him before he could and charged energy for his own attack. "CHAOS… BLAST!"

Everybody in the Commander Centre covered their eyes as the intense blast of light blinded them. When it was over, they could see Devil Doom scrambling desperately to keep Shadow away.

"This is the end of you!" Shadow shouted, charging one final Chaos Spear. He fired it. "And the end to my cursed past!"

As the spear struck Devil Doom, he began to writhe and fall down towards the city. "Im… Impossible! I am the supreme being that rules the universe! I am the immortal lifeform! I am the ultimate power! Gaaaah!" Devil Doom continued falling, his body falling limp and his eye closing as he crashed down to the streets below.

In the Command Centre, silence washed over everyone. Then, a single soldier shouted, "HE DID IT!" and that was enough to send the room into an uproar. People began hugging and high-fiving, the news was spread to soldiers stationed all over the world, and the President finally let out the breath he was holding.

However, Commander Tower wasn't ready to celebrate just yet. He noticed on the monitor that Shadow was now standing atop the Black Comet. Then, Shadow used Chaos Control, warping the comet somewhere… Suddenly, he asked one agent, "Do we have control of the mainframe back from the Black Aliens?!"

The agent stopped her celebrating and stammered, "Uh, y-yes, sir. Miles Prower helped us-"

"Send the launch codes to the ARK right now! Hurry!"

The agent jumped to it and started mashing keys. The President was about to ask what he was doing, before a communication came in from one of the soldiers aboard the ARK. The Black Aliens were suddenly retreating, and they were able to make contact with the surface again. And, even more significantly, the Black Comet was back in space, placed right in the Eclipse Cannon's firing path.

"Receiving a live feed from one of our soldiers!" The monitors displayed an image of the Black Comet drifting in space below the ARK, heading towards it. "Report from Blue Falcon, sir! Shadow has just been sighted at the Eclipse Cannon's controls!" an agent reported.

"Tell him to stand down!" Tower ordered.

"The codes have been transferred, sir!"

Tower nodded, and then waited a few seconds. Then, the Eclipse Cannon began to glow. Energy was gathered at the base of its barrel, and then was fired at the Black Comet, shattering it to pieces that scattered in every direction.

With that, the celebration was in full-swing. The alien leader was dead, and their flagship was destroyed. Reports started coming in that the Black Aliens were falling, not by GUN's hands, but simply that they were toppling over on their own.

Now, Tower could finally breath that sigh of relief. It was truly all over. He felt a hand on his shoulder, and turned to face the President.

"How ironic…" the President began. "After the way we all treated him, he saved us all in the end. We were all wrong about the Professor."

Tower had no response. He simply hung his head, ashamed at his actions… and afraid of what these new revelations meant. "He was a hero," Hope said. She was smiling. "My father always said he was… but I didn't believe him. I lumped him in with my uncle, but now…" Hope took in a deep breath, and let it out. "Now, I have even more reason to stop Doctor Eggman, and restore our family's good name!"

The President nodded. "Let us pay homage to Professor Gerald. Let's work to ensure peace and prosperity for a brighter future! What do you say, Commander?"

Tower looked over to Hope, who smiled back at him and nodded. He looked over his troops, who were still celebrating in the Command Centre. Then he turned back to the President. "Excellent idea, Mr. President. But before that, there's one more thing we must do."

Hope tilted her head. "There is?"

Tower circled round and descended to the lower level of the Command Centre, Hope following after him. "Professor Gerald's shed some light on truth behind Project: Shadow, but not everything is crystal clear just yet." He approached one of the consoles. "I have to know. Otherwise, I can't continue being GUN's Commander-in-Chief."

Hope frowned. "But isn't it enough to simply work for creating a better future?"

"… If I don't even know who my enemies are, how can I be expected to lead anyone? Project: Shadow… This dark chapter in GUN's history must be closed, before it's completely lost to time." Tower sighed. "And I won't deny a level of personal interest to see this case finally come to a close… Hope, would you please lend me your expertise, and help resolve this matter once-and-for-all?"

"… Okay, Commander!" Hope hopped into a seat and logged into the terminal. "Let's do this! Let's bring those accountable for Great-Grandfather's death to light!"

The President watched as the two began to work, when he received a sudden transmission from the ARK. "Hello?"

"Finally, we got through!" It was Vector's voice. "Hey, we found the data you were looking for! Did you see?"

"Yes. We all did, and I thank you deeply for your efforts. You will forever have my gratitude."

"Aw, it was nothin'! So uh, now that the Earth's no longer in danger, I was thinkin' we could talk about, y'know, the payment?"

The President froze, and then let out a hearty laugh.