Be All My Sins Remember'd

"Be All My Sins Remember'd" is the eleventh episode and midseason premier 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 to track their ships and destroy them using the newly acquired plasma beam weapons on their ships. In response the Asurans retreat to their homeworld with the future prospect of returning in strength. To prevent this, 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 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 the Wraith 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 Asuran core drive given to the Atlantis Expedition by Niam's faction to find the locations of the 37 Asuran ships in the Pegasus Galaxy.

Plot
Lieutenant 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 Asuran 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. Lieutenant 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 Colonels Abraham Ellis and Steven Caldwell and the newly acquired Asgard plasma beam weapons. Doctor 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.

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 warship. 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 Replicator nanite. 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 Asuras 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. The First Atlantis Reconnaissance 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 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 ship. Larrin reveals her ship has encountered a human world razed by the Asurans. Sheppard offers Atlantean assistance to repair Traveler ships in return for cooperation in the coming attack on Asuras. 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 Rodney's new creation greets him with a cordial "Hello". Rodney tells Zelenka it was easier to create the human-form as that was what the machine was designed to do.

The Jumper with the First Atlantis Reconnaissance Team returns to Atlantis, Teyla prepares to go to 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 Asurans. The replicator 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 Asuras 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 Asuras and the battle begins. FRAN beams down in one place. McKay, Dex, 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 warship attempts to escape into hyperspace but is destroyed by drone weapons directed by Sheppard. A Traveler 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, Dex, 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 Asuras from the Ancient database before accompanying Sheppard for a late lunch.

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

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.

McKay deleting the Replicator homeworld from the Ancient database

McKay: OK, 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.

Background notes

 * Teyla Emmagan announces the "Previously on Stargate Atlantis" in the beginning of the episode.
 * This episode takes place around two months since the events of "Missing", since Teyla learned she was pregnant by the end of the episode and knew about the pregnancy for two months.
 * The title of this episode, as well as the title of the preceding episode, "This Mortal Coil", is from Shakespeare's Hamlet, Act III, Scene 1, the famous "To Be or Not to Be" soliloquy:
 * To sleep: perchance to dream: ay, there's the rub;
 * For in that sleep of death what dreams may come
 * When we have shuffled off this mortal coil,
 * Must give us pause: there's the respect
 * That makes calamity of so long life;
 * [...]Soft you now!
 * The fair Ophelia! Nymph, in thy orisons
 * Be all my sins remember'd.


 * Lt. Kemp (Niall Matter) was introduced in the season 4 episode Tabula Rasa. It is revealed in this episode that he leads his own team.
 * In a deleted scene, Caldwell and Carter conversed in Hermiod's former work station, speculating he was killed during the extinction of the Asgard on Orilla. It was also revealed that Caldwell was once married, but was divorced.

Goofs

 * 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 ships are flying towards the origin of the shots at the same time while not firing.

Productions

 * Even though Elizabeth Weir made an appearance at the end of the episode, Torri Higginson was not credited until the closing credits.
 * The Nielsen household ratings for this episode was 1.4, the highest rated Stargate Atlantis since "First Strike", which achieved 1.5.