Chapter 3: Whispers in the Dark

'Evacuate all holding cells according to Protocol 7. This base has been disabled: calling on all occupants of the upper levels to report immediately to the main deck. Level Zero has been lost'.

Archie cursed and started pacing as much as the small room would allow. The weight of the gun had begun to make his shoulder ache. So that was that. Five hours of silence from the bridge and nothing left to show for it. He gave another kick to the sealed door, more out of frustration than any hope that it would listen to him and spring open - not that he hadn't asked enough times already.

Archie spun around on his heels to check if the ship's movements had damaged the cargo in any way, but it looked good as new. Well actually, it looked dead old: the container was scratched and worn from years of travel, every bit of it probably as eventful as this journey had turned out to be. At least no one could say he'd slacked off at the end. There was that.

Another explosion rang out from somewhere close by, sending shockwaves up through the floor and making Archie flail backwards as he lost his balance. He hoped to God this room was as inconspicuous as the Captain had assured him: it was supposed to look like nothing more than a store room from the outside and if there was anything people weren't looking for in a state of emergency, it was cleaning supplies.

Two heavy thuds on the metal door shook Archie forcefully from his thoughts. Spinning around, he raised the gun shakily, waiting for an attack with baited breath –

Only to see the light of the intercom flash red.

Archie yelped in surprise and only wasted a second before jamming his finger onto the button.

'Hello? Is someone there?' he asked in a high voice, clearing his throat halfway through to settle on something deeper. 'Identify yourself!'

'Hello, hi! I'm the rescue team' said a faint voice from the other side of the door. Archie felt his body slump forward in relief to lean against the door, the gun slackening in his arms.

'I'm Archie. Is it clear out there?'

The feed went silent for a moment, only to be broken by a strange whirring sound.

'Hello? Are you still there?'

'Yes, sorry, one second ….' the voice grunted, clearly concentrating. 'Have you got the cargo in there by any chance?'

'It's safe' he confirmed. 'I think they must have given u' –

'Right, Archie. You might want to step back'.

His eyes widened and he stumbled backwards just in time to avoid the door exploding off of its hinges. Slowly, it teetered and fell forward to crash on the floor in front of him. Archie tried to make out a figure through the smoke.

'Sorry about that, I've only borrowed this' his rescuer said, waving a metal probe apologetically.

'B-but...' stuttered Archie in bewilderment. 'You're just a kid!'

'I'm nearly twelve' argued Harry, his eyes narrowing.

'But how did you even get here? This is a military ship!'

'You sent out a distress call: something about precious cargo?' asked the black-haired boy, eyebrows raised.

'Right!' said Archie, turning back into the room and typing in the code for the mobile setting on the interface. When the light went green, he spun the capsule on its wheels so the narrow end was facing the open doorway. Harry grabbed it at the top and they somehow managed to manoeuvre it over the fallen door and into the hallway - the eerily quiet and obviously abandoned hallway.

'Where's your ship? Your people?' he asked Harry as they raced down the corridor to the cabin doors, the sounds of a nearby explosion reverberating above them.

'It's on this floor' panted Harry, running backwards and looking over his shoulder as they guided the container. 'But speaking of people' –

They slowed to a stop and Harry opened the door out onto Deck 0.

'Er…never mind, then' said Harry, looking around him at the empty platform. He paled slightly at the sight of the scorched flooring and the obvious hole blown into the stairway on their left. No Amy and Rory, however.

'They should be around here somewhere' he told Archie, hopefully coming off less worried than he was because the young brown-haired soldier looked ready to collapse as it was. 'Wait here, I'll go find them' –

'Don't just run off! Do you know how many of them are still on board? Kid, wait!' –

Harry was too busy sprinting across the cavernous room to listen. He opened the main doors to find an identical row of bunks and storage rooms, listening at each closed door for signs of life and trying not to panic.

He almost missed the glass doorway in his haste and had to fling himself backwards to avoid being seen. Crawling close to the floor, he pushed the door open as quietly as possible. An immediate flood of sound greeted him and he found himself on a narrow platform built around the four corners of a large hall down below. Stacks upon stacks of storage crates were piled up one on top of the other and leaning over, Harry could see hooded figures – at least a hundred of them – breaking each one open and tossing their contents to the floor.

'Harry!'

The low hiss had come from his left, where Amy and Rory – hopefully just under stress and not furious at him for wandering off – were both handcuffed to railings on the corner of the platform. Harry grinned in greeting, staying close to the ground as he made his way over to them.

'What have we said!' whispered Rory, having no problem demonstrating his anger despite the low register. 'No running off, especially on invaded war ships' –

'We can yell at him later' whispered Amy tensely, silently jerking her head towards the hooded figures who were working their way through the containers faster than she would have liked.

Harry tried to look suitably apologetic as he turned on the sonic to release first Amy's cuffs, silently praying that the acoustics here were rubbish.

'It's not working!' he whispered in frustration when the russet red metal refused to break open.

'I knew there was something odd about them' said Rory, looking worryingly down below them. 'Who uses a key in the 82nd century?'

'A key?' asked Harry. 'Where is it?'

Amy and Rory communicated silently – something which always annoyed Harry to no bounds – and seemed to come to some sort of agreement.

'Harry, it's time to go back to the TARDIS' said Amy very seriously. 'You remember where we left it? – By the dining hall' –

'What? You want me to just leave you here?' asked Harry in disbelief.

'We want you to wait in there until we or the Doctor can come and get you' said Rory.

'No way! I can help!' hissed Harry quietly. 'I'll get you the key, where is it?'

Almost imperceptibly, the pair shifted in the direction of the room down below, their eyes widening as they caught on to Harry's triumph.

'Don't you dare!' –

Harry ignored her, along with the guilty feeling he got in his gut whenever he disobeyed Amy or Rory. Carefully he crawled to the adjoining path against the wall, where a small circular protrusion in the floor jutted out enough to let him look down below (with any luck, unnoticed).

Harry had yet to come face to face with whatever group had invaded the ship and hanging over the edge, he still couldn't make out a face beneath their dark cloaks and hoods. Harry also hadn't heard a single voice down below. They seemed to be working silently, aside from the sounds of their less-than-delicate search. He found it strangely unnerving. On the opposite side of the room, they had broken into a container full of weaponry and a dozen metal trunks. The centre of the room had been all but emptied already and directly below him, two of the figures were standing silently, surveying what were probably their underlings.

One of them moved suddenly and looked up in his direction, Harry pulling his head away just in time. Breathing heavily, he froze just to be sure he hadn't been seen. Once the threat of gunfire had passed, Harry squirmed into the same position. It had only been a glimpse but he'd seen it as the figure turned: a flash of red metal tied onto the side of the creature's robes. If he leaned slightly to the left he could see the key, hanging from the belt of his (or her) robe.

How to go about this? Harry looked over at the Ponds who were sending him daggers with their eyes from the corner of the platform. Wincing slightly, Harry mouthed 'It's okay' and shifted, leaning forward to free his hand over the side of the platform. He hadn't planned on showing either of them, especially not at a time like this, but he was desperate, wasn't he? He could do this.

Stretching his hand out over the side, he stared hard at the key down below, biting his lip in concentration. For a second he worried that it wouldn't work but then he felt it, bubbling up from somewhere deep within his core and despite the urgency of the situation he smiled at the sensation.

Focusing intently, he could have whooped with excitement when the key slowly slipped itself loose of its tie and floated upwards through the air. Time seemed to stand still as it rose, those below still oblivious. Harry could feel Amy and Rory's shock coming off of them in waves from a few feet over as he grasped the cold metal in his flailing hand.

Hurriedly, he crawled back to the pair and tried not to meet their eyes while he unclasped their handcuffs.

'I also found the cargo' he whispered, which made Rory choke down a bemused laugh as he rubbed his sore wrists.

.

.

.

'I thought you'd left!' exclaimed Archie, who they found pacing in front of his charge, gun in hand, on the main deck. 'We need to get out of here. The vessel has to be maintained at a constant temperature and air pressure or it could open before it's set to'.

'So this is it?' asked Amy curiously, stepping up to the engraved capsule to examine the lid. 'All this fuss over a glorified wardrobe'.

Archie made a garbled, choking sound. 'This is the earth's most sacred religious artefact' he finally settled on. 'It's over five thousand years old and perfectly preserved'.

'So why does the military have it?' asked Rory.

'We're the Church' said Archie as if it was self-evident.

'What's inside?' asked Harry.

'Nobody knows, do they?' he answered. 'It's supposed to be the Word of God. Only bishops and up are allowed to know what's really in there'.

'Well, that certainly sounds like the Church' muttered Rory.

The ship groaned and shook as another alarm rang out from where Amy and Rory had been held. They'd sealed the door shut behind them but none of them knew how long it would hold against an assault.

'Where's the Doctor?' asked Harry.

'He went up to Level 7 to the captain's berth' explained Rory. 'The main engines went down so he's trying to release some dead weight to keep us in orbit'. The door started shaking against a sudden barrage of gunfire from the other side.

'We should work our way up, then' said Amy. 'I assume you know how to use that thing?' she asked Archie, pointing at his machine gun.

He shifted uncomfortably and Harry groaned.

'I thought you were the guard!'

'I'm a conservator!' he protested. 'I'm just here to do maintenance every few days. They sealed the doors shut while I was working'.

'Er… Amy?' called Rory, pointing to the large glass windows across the way. 'Is it just me or does that look like levels one through seven?'

They all turned as one to see the ship, still colossal even without its bottom floor, floating in deep space and getting further and further away.

'They've cut us off' gasped Archie. 'I'm supposed to protect the cargo at all costs and they just threw us away!'

'The Doctor wouldn't just leave us' Amy assured him. 'For now, let's get back into the TARDIS where it's safe' –

The metal door being bent outwards from the centre by blunt force swallowed up the rest of her words.

'I second that' agreed Rory, pushing the other end to Archie's as they all made a run for the blue police box, which was standing in the beverages section of the dining hall where they'd left it.

They'd only just rolled the load inside and slammed the door shut before a dozen of the robed people came storming through the remains of the doorway, red lights crackling menacingly in their hands.

'It's…. It's bigger' said Archie, looking sick. 'We're inside and now it's bigger'.

'You get used to it' said Harry, but any further explanation was cut short by the ringing of the telephone, which Amy promptly picked up.

'Hello, Doctor. Anything you want to share with us?'

'Pond! Wonderful. If you haven't already noticed, I had to disable your level, but not to worry: I've set the TARDIS to auto-pilot. It'll take you straight to me. All you need to do is hold onto the telepathic flight controls and she'll do the rest. See you soon!' Click.

All four of them were reeling by the time the TARDIS came to a halt.

'I'll never complain about the Doctor's driving ever again' groaned Rory, steadying himself on the railing.

'My mind kept wandering, okay?' glared Amy.

Opening the TARDIS door, they could hear gunfire echoing throughout the ship. Amy and Rory had already slipped outside when Harry looked back to see Archie standing uncertainly by the container.

'Aren't you coming?' he asked. 'You don't know the Doctor, but he probably has everything under control. Even if he doesn't look like he does'.

'It sounds rough out there' said Archie, visibly defensive. 'It's my job to keep this thing safe. It's the only reason I'm here!'

'But you don't even know what's in there' argued Harry, bewildered. 'Actually, you know what? Suit yourself' Harry gave up, following the others out into what looked like a viewing station at the top of the ship.

Archie was left standing awkwardly in the console room for some time, his head ringing from their bumpy ride. Eventually he opened the door to peek outside and was greeted by the deafening sounds of a grenade going off down the hall. He turned to look at the capsule on the TARDIS floor, by now looking the worse for wear, and clenched his gun feebly. Swearing, he threw open the TARDIS door and ran out into the blaze before he could change his mind.

Nobody was there to hear the faint beeping of the capsule as its digital interface began to glow red.

Nobody saw it click open either, releasing gas into the TARDIS with a long, drawn-out hiss.

.

.

.

'Companions of the Doctor, I'm to escort you to Operation Control' announced a surly faced soldier, saluting the Ponds and looking strangely at Harry.

'Is the fighting still going on?' asked Amy as they walked down a narrow corridor and past several armed guards.

An answering explosion from somewhere below cut the soldier's response short as they walked through to a bright room with a ring of machines around the walls and a large glass window looking down at the rest of the ship.

'Not for long' smiled the Doctor, spinning around energetically on a wheely chair to face the three of them. 'Father, at ease' he said to the soldier with a mock salute.

'Father?' questioned Harry.

'Well, not my Father' the Doctor assured him. 'Maybe somebody's father, but he's far more likely to be my great great grandson times a thousand if anything. In this case, father of guns and hand grenades, I should think'.

'Do you know who they are…the hooded people?' asked Amy. 'They didn't say a word to us, they just threatened us with their creepy hand magic'.

Harry cringed at her choice of wording but no one else seemed to notice.

'Ah, yes. That would be the headless monks' nodded the Doctor, turning back around to the computer in front of him.

'You mean like at Demon's Run?' asked Rory.

'Not exactly. They're a different faction. They probably haven't even heard of me yet, let alone the Silence. One more second and …. There' he finished, as hundreds of files flashed alternately across the screen. Picking up a microphone on the control desk, he leaned back in his chair jauntily and turned it on with a flourish.

'Ahoooooy!'

The Doctor's voice reverberated throughout the ship, headless monks and the ship's crew alike pausing momentarily in the middle of their fighting to listen. With the loss of gunfire, the ship fell silent.

'That's more like it' said the Doctor. 'Now everybody with ears, listen up. Everyone without, you can just take your orders from the Abbots in charge who are probably holding up in that great big ship thirty-two miles away – yes you! Hello! Did you get my present? See, I've spent the last half hour decrypting the ship's terrific emergency censors and what do you know? That box you're so intent on finding is hidden on the wing we just expelled - and I've just sent you the floor plan'.

The door burst open and a giant of a man in uniform came charging inside with a dozen soldiers in his wake. He pulled out his gun and drew it on the Doctor, who just winked and held up a single finger for the man to wait.

'So let's re-evaluate, then. You're outnumbered, you've already lost half your faction and your incentive just floated away with the rest of the reinforcements. Oh, and let's not forget the Type 12 Teleportation bands that got you on board in the first place. I'd say they have enough collective energy for one more trip, wouldn't you?'

Everyone in the control room held their breath as they waited for the fallout of the Doctor's speech. Then a multitude of cheers replaced the gunfire from all over the ship.

'How dare you, Doctor' snarled the soldier, who still had a gun pointing threateningly at the Time Lord's head and was the only one not to relax at the monks' departure. 'I gave you control on good faith and you hand the vessel over to our enemies…without even consulting me!'

'Put the gun down, Archbishop. You're embarrassing everyone' said the Doctor, unconcerned. 'The Word of God is safe and sound in my TARDIS, isn't that right?' he asked the three watching in a corner of the room.

'He's telling the truth' said a new voice in the doorway. A ruffled looked Archie flinched visibly as a dozen guns pointed at him, but he managed to return Harry's smile, if a little uncomfortably.

'Brother Archibald – you swear that the cargo is safe?' asked the Archbishop, letting out an almost imperceptible breath when the young conservator nodded.

'How did you know?' Rory asked the Doctor curiously.

'This database controls the entire ship. I saw the seal break on the storage room and since the monks were still charging ahead, I knew you must have found it. Great use of the sonic, Harry, I meant to say! I can't wait to find out what's inside' the Doctor said, standing up and rubbing his hands together appreciatively.

'Don't move, Doctor' said the Archbishop. 'Father Farrow, keep your weapon trained on him' he ordered a redheaded soldier to his left. The Doctor frowned and Rory and Amy exchanged worried glances as the man in charge held a transmitter up to his mouth.

'This is the Archbishop in command of Flight 59B. Enabling all emergency systems on port-side. Prepare to launch in five minutes. This is a Code Brassard'.

'That's not necessary!' protested the Doctor. 'They've gone and they don't have enough energy to get through your shields again' –

'I can't afford to take that risk, Doctor' said the Archbishop.

'What is Code Brassard?' asked Amy, recognising the cold look of fury growing on the Doctor's face all too well.

'He wants to blow up Level 0 along with the five hundred life forms still there' said the Doctor icily. 'But he knows very well that I'm not going to let that happen'.

'You have no weapons, Doctor. It's done already' said the Archbishop.

'Never really saw the point of weapons' rebutted the Doctor. 'But why fix a problem when you can just blow it up, eh?'

'Don't vex me, Doctor. Not now. I've just lost dozens of soldiers'.

'You can save the universe with any old thing these days and believe me, I've tried them all' continued the Doctor as if he hadn't heard the other man. 'A well-timed banana, a teaspoon and an open mind – of course nothing beats a good' –

Harry, catching on, tossed the sonic to the Doctor who caught it deftly and extended it out to the interface at his side.

'- Screwdriver, now does it?' he finished, grinning at Harry and extending the sonic.

'Put it down, Doctor' grunted the Archbishop furiously.

'You may not know me very well, but I know you' said the Doctor, his eyes darkening. 'Oh yes, I've met you in every corner of the universe and never, not once, has this ended well for you. Because I've seen your cards and they're rubbish. See, in between bringing about a ceasefire and checking my email, I built in my own emergency protocol' said the Doctor, jerking his head to the interface. 'You blow up the last of the monks and your own weapons system self-destructs. It won't kill anyone but your ship will be next to defenceless to the next army that comes knocking'.

'Father, the vessel is on board' said Archie meekly. 'Maybe you should' –

'Quiet, boy!' yelled the Archbishop. 'I will not have you intimidate me, Doctor. We have been at war for long enough. Farrow, shoot the boy'.

'No!'

Amy cried out and tried to stand in front of Harry but the soldiers on either side pulled her back by the arm and centred their guns on the married couple. The redheaded soldier had paled visibly at the order, but with shaky movements he raised his gun and held it up to Harry's head.

'Don't you dare!' yelled the Doctor.

'It's your choice' said the Archbishop. 'In one minute, our missiles are going out. It's up to you whether or not the boy dies too'.

'Stop it! Would you kill a child just because he tells you to?!' Rory screamed at Farrow, whose lip was quivering. The soldier kept his eyes on Harry's though, bright green and wide as they skirted from Farrow to the Doctor anxiously.

'It's not too late' said the Doctor dangerously, looking only at the Archbishop. 'You can stop now and go in peace. But if you harm Harry in any way, I will destroy you'.

'Let's give you thirty seconds, shall we?' asked the Archbishop, taking up his transmitter again. 'This is operations, preparing to launch at my word' –

'Put it down, Father!' shouted Archie, who so far had been watching the proceedings with frozen horror. The priest turned his gaze slightly to see the young conservator pointing his gun at him with clear intent and started to lower his own.

'Hold steady, Father' said the Archbishop. 'It is an honour to die for God's word'.

'Doctor' whimpered Amy in fear.

'Choose now, Time Lord. The life of a child or those of terrorists' -

'It's okay, Doctor'.

It was the last statement that shook the Time Lord to his core. He turned his head around to look at Harry who seemed almost – accepting? The Doctor's jaw clenched and he prepared to make his choice –

'STOP THIS NOW!'

The entire room turned in the deafening silence that followed the outburst.

An elderly man stood in the doorway, his skin engraved with age lines. He was dressed in white robes not unlike the clergy of another time and carried a quiet strength in his stature despite his frailty. Immediately, the Archbishop's jaw dropped in shock and he faltered.

Archie looked over his shoulder in confusion at the stranger, unsure whether or not to lower his gun on Farrow – putting it up had been traumatic enough.

'Is this what the House of God has come to?' asked the elderly man, now exhibiting that rare skill of being able to emit fury while barely raising his voice. 'Murdering children?'

Harry had to repress the urge to remind them all that he was nearly twelve and instead tried to make sense of what was going on. From across the room he could see a look of surprised wonder on the Doctor's face, his screwdriver still held up to the controls.

'Put the weapons down' said the man quietly. The soldiers looked to the Archbishop who nodded vigorously and lowered himself to a kneeling position, his head bowed. Slowly the soldiers lowered their guns, sharing questioning looks.

'I'm sorry, but who are you?' asked Rory, once he felt he'd glared enough at the soldier who'd been ready to shoot Harry.

'Isn't it obvious?' asked the Doctor, popping his screwdriver back into his pocket. 'He's the Vessel. And may I say it is an absolute pleasure to meet you' he said sincerely, walking forward to shake the serene man's hand. 'Stasis chamber, was it?'

'He's not the vessel' denied Archie. 'The vessel is…it's not… you're not, are you?'

'I'm afraid I am' said the old man with a glint of humour behind his serene façade. 'A prophet, to be exact. The last of the old order'.

'Jesus Christ' whispered Archie, before blushing furiously at his wording.

'Wait, why were you put in stasis?' asked Harry. 'You said the capsule was shut for five thousand years' he reminded Archie.

'As I got on in years, I agreed to be preserved and reawakened by the Papal mainframe at a time when they most require guidance' explained the Prophet. 'I assume whoever was meant to look after me wasn't expecting whatever warfare has taken place here today'.

'There is one thing I'm curious of' continued the prophet, looking to the Doctor curiously. 'I woke up in an extraordinary room'.

'The Vessel, in my TARDIS' muttered the Doctor excitedly. 'Ah, yes, well you would be curious. I can give you a tour if you like, although I'm sure you'll want to be getting back to your stasis chamber'.

'Actually, it would seem I have enough to be getting up to in the here and now, don't you think?' he asked, looking over at the remaining soldiers.

The Doctor nodded solemnly and clasped his hand once more before they said their goodbyes to Archie. Dazed and pleased, the conservator agreed to stay on with the Vessel as planned, still reeling with the revelation of exactly what he'd been maintaining for the past few months.

Back at the TARDIS, the Doctor ran in ahead to examine the stasis chamber he'd accidentally commandeered so it was easy for Amy and Rory to corner Harry before he could step inside.

'You know we're not going to forget what happened' said Amy, eyes narrowed. 'Learning the art of telekinesis in our spare time, are we?'

Harry felt unaccountably nervous, having gotten over most of his shyness years ago. But Harry's abilities had always been a sore spot around the TARDIS, a shadow which followed them around. No one could ever explain to him what had happened with the Angel when he was eight and he had a feeling that it made them all uneasy to be so in the dark. It was also the only question the Doctor had ever failed to answer for him, and not for lack of trying.

'It was an amazing thing you did' said Rory with a begrudging smile. 'Just don't keep secrets that big from us, okay?'

'Okay' said Harry, taken aback by their reaction.

'But if you ignore us like that in a dangerous situation ever again' –

The ensuing lecture went on longer than Harry could have expected – didn't people usually want to rest after being kidnapped/restrained by religious fanatics? He didn't really mind, though. It was the sort of thing parents did.

Just as he was stepping inside after them, another voice pulled him back.

'Harry?' asked the prophet. 'May I have a word before you go?'

'Yeah, sure' said Harry awkwardly, not sure what the earth's most famous religious figure would want with him.

'I have a message for you' he said and Harry raised his eyebrows suspiciously. 'From..?' he asked but the older man seemed not to have heard him.

'The darkness… that resides inside you, in your very soul…. It goes hand in hand with your power and you cannot fight it'.

'Darkness?' asked Harry sceptically, not enjoying the prophet's intense gaze. 'What are you' –

'Harry, are you coming?' called Rory from inside the TARDIS.

'I'll be in in a second' he called back through the open doorway, his voice breaking slightly on the last word. When he turned back around, Harry found himself alone in the corridor and the dramatics of that move alone might have convinced him that the prophet's so-called message was nothing but theatrics.

But then why had even the Doctor - the ultimate sceptic - seemed impressed by the man? Despite himself, the Prophet's words had struck a chord in Harry, planted a seed of doubt that he would never quite be able to shake off.