Be All My Sins Remember'd

"Be All My Sins Remember'd" is the eleventh episode of the fourth season of Stargate: Atlantis.

Synopsis
With the Asurans undeterred in their effort to wipe out Human populations to defeat the Wraith, the Atlantis expedition now have a means of tracking their ships and destroy them using the newly acquired Asgard plasma beam weapons on their ships. However, their efforts mean that the Asurans have to retreat to their homeworld, only to come back again in bigger numbers. In order to stop them, the Atlantis expedition, Wraith and the recently discovered Travelers must work together to stop the Asurans once and for all.

Previously on Stargate: Atlantis
The Asurans were induced to attack the Wraith by Dr. Rodney McKay, who reactivated that command in their base code. The Asurans adopt the effective anti-Wraith strategy of destroying Human colonies the Wraith feed on. Both McKay and Todd attempt to rescind the attack command by modifying the Wraith computer virus originally used to suppress the attack command thousands of years ago, but without success. McKay used the Asurans Core drive given to the Atlantis expedition by Niam's faction to find the locations of the 38 Aurora-class battleships in the Pegasus Galaxy.

Plot
Lt. Colonel John Sheppard and his team ready a mission to planet M9R-373 to evacuate its human inhabitants, the Sion. The world is in the path of the Asurans advance. Sheppard is anxious that they have had little or no contact with the populations they are evacuating and needs Ronon Dex and Teyla Emmagan as much as possible, despite Teyla feeling a little ill. The Stargate activates and people start coming through to Atlantis. Lt. Kemp, managing the evacuation on the far side, requests Teyla transit through to convince those opposed to the relocation. Before this can happen, the Asuran attack begins. The Gate deactivates and Kemp and the remaining 2,000 people are lost.

Daedalus and Apollo arrive from Earth with Colonel Abraham Ellis and Colonel Steven Caldwell and the newly acquired Asgard plasma beam weapons. Dr. Rodney McKay reports a lack of progress on the anti-Asuran computer virus. This leaves Plan B, which is to use the new weapons and use brute force. McKay points out that Plan B is not optimal as while space can incapacitate the Asurans they may yet be recovered and reactivated by inquisitive space-faring civilizations. After a heated argument between McKay and Ellis a compromise is reached: if McKay cannot produce a working virus in ten hours, the ships will begin conventional strikes.

Once McKay has left the room Carter, furious at Ellis being arrogant and rude to McKay, informs him in no uncertain terms that if he ever speaks in that way to someone under her command again then he will no longer be welcome on Atlantis. Ellis, somewhat taken aback but realising he was indeed out of line, accepts the rebuke.

McKay and Todd, the captured Wraith, continue work on the virus. Todd doubts that it can be done in ten hours and is proved correct. Daedalus and Apollo are deployed to intercept an Asuran Aurora-class battleship. The enemy warship is easily destroyed with the Asgard weapons as soon as it exits hyperspace. Caldwell expresses confidence in the new strategy but Colonel Samantha Carter cautions that the Asurans have a history of adapting quickly.

Within a week the two ships destroy a further six ships. However, Caldwell's success is its own undoing. The Asuran fleet begins to withdraw to Asuras, their homeworld. The Tau'ri do not have the strength to attack the planet and the consolidated fleet by themselves, but neither can the Asurans be allowed time to rebuild their strength and adapt. Interest in McKay's anti-Asuran program returns to the fore but the doctor is convinced he cannot deliver it.

McKay presents another possible solution to Sheppard and Carter. He references the Anti-Replicator gun (ARG) which disrupt the bonds between each Asuran nanites. As the Asurans are likely resistant or immune to the ARG's effects, McKay proposes to strengthen the inter-nanite bonds, causing every nanite to coalesce into one immense blob so dense as to incapacitate the nanites, and the Asurans by extension.

McKay also conceives a way to induce this without the need to infiltrate Asurans and upload a program. The vector would be a block of nanites, serving as a magnet to other nanites, created by the Lantean nanite creation machine abandoned on Atlantis. The block would be delivered to the planet surface where it would do its work without further intervention. The only issue is the effects will take some time to reach into orbit and disable the Asurans on board ships. If even one enemy ship escapes all will be for nothing.

The two human ships are insufficient to block the Asurans from escaping. On Sheppard's suggestion the humans approach Todd, who tells them he can easily send at least twelve Wraith ships in support. Todd is adamant that his people can only be convinced by himself personally. Sheppard's team, minus McKay, plus Todd, take a Puddle Jumper to a fleet of Hive Ships near a Spacegate. Sheppard warns Todd not to betray them. The Jumper is given permission to land in one of the ships. When they land the humans, especially Ronon Dex, are stunned by Wraith warriors.

Back on Atlantis, McKay and Dr. Radek Zelenka cannot make the block. Too many of the nanites' protocols have been disabled for the block to maintain cohesion. Zelenka is summoned to Section Seven where a Naquadah generator is malfunctioning. While Zelenka is gone McKay realizes a potential solution and begins work on it.

Elsewhere, Sheppard regains consciousness and is greeted by Todd, who says the Wraith needed to negotiate alone. Todd reports seven Hive Ships have agreed to participate. The remainder will not because of the risk and a shortage of Wraith Queens.

As the Atlantis team prepares to depart the Traveler Aurora-class ship commanded by Larrin arrives near the Wraith fleet though not in time to see them leave. Sheppard boards the Traveler generational ship. Larrin reveals her ship has encountered a human world razed by the Asurans. Sheppard offers Atlantean assistance to repair Traveler generational ships in return for cooperation in the coming attack on Asurans. Larrin promises to bring the offer to the Traveler Governing Council, but admits even if the council is in favor ships will be able to decline on an individual basis.

Back on Atlantis, McKay successfully completes the nanite vector, not as a block, but as a Human-form Replicator. Zelenka is subsequently shocked when McKay's new creation greets him with a cordial "Hello". McKay tells Zelenka it was easier to create the human-form as that was what the machine was designed to do.

The Jumper with Sheppard's team returns to Atlantis, Teyla prepares to go to Dr. Jennifer Keller for a checkup because of the stun. When Sheppard asks why this stun is any different Teyla reveals she is three months pregnant. Sheppard is both surprised and infuriated; he takes Teyla off active duty to minimize further risks to mother and child. Ronon congratulates Teyla and confides that he knows Kanaan is the father by the way she talks of the Athosian. Ronon agrees to accompany Teyla to the check up.

Sheppard tells Carter of Teyla's pregnancy, who in turn tells him of McKay's human-form replicator. McKay assures the flustered Sheppard that most protocols aside from walking and talking are disabled and it cannot replicate or contact the other Asurans. FRAN takes the liberty of going over McKay's calculations and finds a flaw in the plan. At the current projected rate the nanite blob will not reach critical density before the nanites adapt, take control of the mass, and prevent their own collapse. However, the human-form, shortly to be named FRAN, has a solution.

McKay presents the new plan to his human, Wraith, and Traveler compatriots. The detonation of a half-dozen Zero Point Modules (ZPMs) around the mass will speed compression and prevent the creation of a "Replicator Godzilla". McKay likens this to creating a "Replicator fusion bomb". The planet will be destroyed in the process. However this requires McKay to beam down to the Asuran Core Room to take control of the planet's power grid and overload the ZPMs. While McKay works in the Core Room, FRAN will beam down and begin creating the blob. In space the combined fleet will attempt to prevent the enemy from escaping by targeting hyperdrives. Sheppard accepts a place on Larrin's ship to control its Drone weapons. Ellis is skeptical as the plan is based on information provided by a Replicator. Sheppard counters that they are trusting McKay.

The fleet assembles before the attack. Carter is impressed by the sight. Caldwell tells her he once thought carrying out joint operations with the Russians after the Cold War was strange. The fleet then jumps into hyperspace. FRAN is excited about stopping the Asurans. The prospect of non-existence is a seemingly minor concern to FRAN compared to the opportunity to fulfill its purpose. McKay and Zelenka are taken aback by this nonchalant attitude.

The fleet arrives at the Asuran homeworld and the battle begins. FRAN beams down in one place. McKay, Ronon, and ARG-armed Marines beam down to the Core Room. McKay takes control of the power grid and soon afterwards FRAN begins forming the blob.

In orbit, damage and losses mount on both sides. One Asuran warships attempts to escape into hyperspace but is destroyed by drone weapons directed by Sheppard. A Traveler generational ship and a Wraith hive ship are also destroyed and Todd's ship is nearly destroyed too, but he is saved by the Daedalus which destroys the enemy warship with its beam weapons. As Apollo prepares to transfer power from the beam weapons the enemy warships stop firing as the massive nanite blob gains enough power to draw in the nanites from orbit. With every nanite part of the blob, McKay prepares to overload the ZPMs. Unfortunately, the massive blob destroys the Subterranean power grid and the ZPMs can no longer be overloaded.

Sheppard suggests firing nuclear warheads at the "Replicator Godzilla", but McKay doubts it will work: the blasts have to be timed to the nanosecond to compress the blob as required, something not likely to be achievable with such weapons. Carter reports neutronium is abundant in the planet's soil. The ultra-dense neutronium can be incorporated into the nanite mass by increasing the attraction some more. This would make the mass dense enough to sink all the way to the planet's core where the pressure will implode and destroy the mass. McKay makes the necessary modifications and he, Ronon, and the Marines beam out as the Core Room begins to shake violently. The fleet jump into hyperspace as the planet explodes.

Back at Atlantis the Travelers amicably depart after the expedition is done fixing their Aurora-class ship. The Wraith never showed up at the rendezvous and the Atlantis team assumes they are enemies again, putting life back to normal. McKay happily deletes the Asuran homeworld from the Ancient database before accompanying Sheppard for a late lunch.

In the debris field of Asuras, a single Aurora-class vessel with the remnants of Niam's faction scans for trace Asuran cells and find none. Dr. Elizabeth Weir is glad that they can finally get to work without looking out for the other Asurans.

Notable Quotes
(The colonels beam into Atlantis)

Caldwell: Colonel.

Ellis: Colonel.

Caldwell: (to Carter) Colonel.

Carter: Colonels.

Ellis: (to Sheppard) Colonel.

Sheppard: Colonels.

McKay: What, seriously?

McKay: Our old anti-replicator technology relied on disrupting the bonds between each individual nanite cell. They just collapsed into a pile of dust, right?

Sheppard: We're familiar with the technology, yes.

McKay: Right. Well, the thinking was to always continue down that line. To break the bonds, to turn them off, severe there connections to one another. Because dust we can deal with, right?

Carter: Rodney...

McKay: We do the opposite! Instead of severing their connections we significantly dial up their attraction to one another. We turn each cell into an incredibly powerful nanite magnet. You know, one cell attracts another cell and those attract two more. And as more and more nanite cells bond to the core group the bonds become stronger and stronger and stronger to the point where every cell on the planet in orbit are amassed in this giant super dense blob.

Sheppard: A super dense blob, that's your great idea?

McKay: It is, yes actually.

Sheppard: What do we do with the blob then? Aren't we in danger of creating some Godzilla-size super replicator?

McKay: No, at least not at first. This is not there normal form of bonding. It will take them some time to adapt, to figure out how to function within the new parameters.

Carter: How much time?

McKay: Well, I mean, I hate to speculate.

Sheppard: Oh, since when?

McKay: Look, it doesn't matter anyways because long before that happens they're gonna fuse together so tightly they will be rendered essentially inert. Remember this bond is occurring on a subspace level.

Carter: Which helps them get passed the normally repulsive force between nuclei.

McKay: To the point where their electrons are fusing with there protons and once that starts happening they're toast.

Carter: Yeah, but your talking about Neutron Star levels of density.

McKay: Precisely.

Carter: Wow, it sounds crazy but it could work.

Larrin: We picked up on seven hives orbiting a single planet. Seemed like something big was going down. So, I thought we'd stop by and do a little intel. What are you doing here?

Sheppard: Yeah, well you just missed them.

Larrin: I see that. So, tell me what are you doing here? And better yet, why didn't those hives destroy your puny little ship?

Sheppard: I take great offense to that. But those are all good questions. We should talk.

Larrin: Yes, we should.

McKay: The systems the Ancients had in place were designed to create fully functional humanoid replicants, right?

Zelenka: Yes.

McKay: Well, turns out that trying to create something much simpler is, ironically, much more difficult. In the end I was forced to compromise.

Zelenka: Wait, you're not suggesting that...

McKay: I know it wasn't part of the plan but it was either this or nothing.

(McKay reveals to Zelenka that a Replicator woman is sitting on the nanite creation machine)

FRAN: Hello. Zelenka: Oh my.

McKay: Now well I'm working in the core room, we'll beam FRAN down to the city. Ellis: Wait a minute, FRAN? McKay: It's Friendly Replicator ANdroid. Sheppard: I didn't realize we were naming things! McKay: It noticed that Zelenka and I both had names and um, she asked for one.

(Discussing FRAN)

McKay: It can't die, it's not alive. It's a program. I mean, its consciousness is just a bunch of ones and zeroes. I mean, you can call it "she" all you want but it's still just a thing, a prop, a really advanced radio-controlled weapon. I mean, you don't feel sorry for your bullets, do you, your bombs?

(McKay talking to FRAN about her to-be fate)

McKay: And you're fine with all this?

FRAN: Why would I not be? It's my reason for being.

McKay: Well, I know. It's just that you're gonna cease to be.

FRAN: Yes.

McKay: Well, I just imagined you'd rather keep being than, uh, than not.

FRAN: Certainly you're not worried for me, are you, Doctor?

McKay: No, no, that would be silly.

FRAN: Yes, it would.

McKay: (to Zelenka) Should never have given it speech.

Zelenka: (sotto voce) Yeeeah...

McKay: Carter we are geniuses!

(McKay deleting the Replicator homeworld from the Ancient database)

McKay: Alright, M7R-227, you were a constant pain in the ass. It's good to see you go. (presses a button, the planet designation disappears)

Sheppard: If only it was that easy in real life..

McKay: Area 51 is working on it.

Goofs

 * At the beginning of the episode there is an "offworld activation" not the scheduled or unscheduled kind. There was no IDC transmitted, and the shield was not used. People just started popping in. This goes against all procedure set forth in Stargate SG-1 or Stargate: Atlantis so it can only be a goof.
 * During the execution of the final mission against the Asurans in this episode Ronan Dex was to beam down to Asuras with Dr. Rodney McKay with a "squad" of Marines. A squad of marines is defined as three fireteams of four Marines and a Staff Seargeant or Colonel as squad leader. Not only was there no one of appropriate rank there were only 3 Marines accompanying McKay and Ronan. That's hardly a squad.
 * As with several other episodes, the Spacegates portrayed possess only eight chevrons compared to the nine that all Stargates are considered to have. Most fans (and this wiki) put this down to an oversight on behalf of the SFX team and consider them to have nine-chevrons as far as Stargate canon is concerned.
 * In the early stages of the battle, several Traveler energy weapon shots can be seen and heard firing out of nowhere. This is probably an error as two Traveler generational ships are flying towards the origin of the shots at the same time while not firing.

Nominations

 * Nominated Gemini for "Best Visual Effects" (Mark Savela, Marco Checa Garcia, Sebastian Greese, Shannon Gurney, Paul Hegg, Brandon Hines, Aaron Kramer, Nik Slotiuk, Toby Taplin and Ray Van Steenwyk)

Deaths

 * Lt. Kemp
 * Oberoth (implied)